Expression and secretion system

ABSTRACT

The invention provides an expression and secretion system, and methods of using the same, for the expression and secretion of one fusion protein in prokaryotic cells and a second fusion protein in eukaryotic cells. Also provided herein are nucleic acid molecules, vectors and host cells comprising such vectors and nucleic acid molecules.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a divisional of U.S. application Ser. No.16/821,856, filed on Mar. 17, 2020, which is a divisional of U.S.application Ser. No. 15/690,544, filed on Aug. 30, 2017, now U.S. Pat.No. 10,633,650, which is a divisional of U.S. application Ser. No.13/934,570, filed on Jul. 3, 2013, now U.S. Pat. No. 9,803,191. U.S.application Ser. No. 13/934,570 claims benefit from U.S. ProvisionalApplication Nos. 61/668,397 filed on 5 Jul. 2012, 61/852,483 filed on 15Mar. 2013, and 61/819,063 filed on 3 May 2013, all of which are hereinincorporated by reference in their entirety.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has beensubmitted electronically in XML format and is hereby incorporated byreference in its entirety. Said XML copy, created on Apr. 28, 2023, isnamed 50474-097007_SL.xml and is 119,335 bytes in size.

FIELD OF THE INVENTION

The present invention relates to an expression and secretion system, andmethods for its use, for the expression and secretion of one Fab fusionprotein when the nucleic acid is transformed into a prokaryotic cell forphage display and a distinct or identical Fab fusion protein when thenucleic acid is transfected into an eukaryotic cell for expression andpurification. Also provided herein are nucleic acid molecules, vectorsand host cells comprising such vectors and nucleic acid molecules.

BACKGROUND

Phage display of peptides or proteins on filamentous phage particles isan in vitro technology which allows the selection of peptides orproteins with desired properties from large pools of variant peptides orproteins (McCafferty et al., Nature, 348: 552-554 (1990); Sidhu et al.,Current Opinion in Biotechnology, 11: 610-616 (2000); Smith et al.,Science, 228: 1315-1317 (1985)). Phage display may be used to displaydiverse libraries of peptides or proteins, including antibody fragments,such as Fabs in the antibody discovery field, on the surface of afilamentous phage particle which are then selected for binding to aparticular antigen of interest. The antibody fragment may be displayedon the surface of the filamentous phage particle by fusing the gene forthe antibody fragment to that of a phage coat protein, resulting in aphage particle that displays the encoded antibody fragment on itssurface. This technology allows the isolation of antibody fragments withdesired affinity to many antigens form a large phage library.

For phage-based antibody discovery, evaluation of selected antibodyfragments and the properties of their cognate IgGs in functional assays(such as target binding, cell-based activity assays, in vivo half-life,etc.) requires reformatting of the Fab heavy chain (HC) and light chain(LC) sequences into a full-length IgG by subcloning the DNA sequencesencoding the HC and LC out of the vector used for phage display and intomammalian expression vectors for IgG expression. The laborious processof subcloning dozens or hundreds of selected HC/LC pairs represents amajor bottleneck in the phage-based antibody discovery process.Furthermore, since a substantial percentage of selected Fabs, oncereformatted, fail to perform satisfactorily in initial screening assays,increasing the number of clones carried through thisreformatting/screening process greatly increases the ultimateprobability of success.

Here, we describe the generation of an expression and secretion systemfor driving expression of a Fab-phage fusion when transformed into E.coli, and of driving expression of a full-length IgG bearing the sameFab fragment when transfected into mammalian cells. We demonstrate thata mammalian signal sequence from the murine binding immunoglobulinprotein (mBiP) (Haas et al., Immunoglobulin heavy chain binding protein,Nature, 306: 387-389 (1983); Munro et al., An Hsp70-like protein in theER: identify with the 78 kd glucose-regulated protein and immunoglobulinheavy chain binding protein, Cell, 4:291-300 (1986) can drive efficientprotein expression in both prokaryotic and eukaryotic cells. Usingmammalian mRNA splicing to remove a synthetic intron containing a phagefusion peptide inserted within the hinge region of the human IgG₁ HC, weare able to generate two distinct proteins in a host cell-dependentfashion: a Fab fragment fused to an adaptor peptide for phage display inE. coli and native human IgG₁ in mammalian cells. This technology allowsfor the selection of Fab fragments that bind to an antigen of interestfrom a phage display library with subsequent expression and purificationof the cognate full-length IgGs in mammalian cells without the need forsubcloning.

SUMMARY

In one aspect, the invention is based, in part, on experimental findingsdemonstrating that (1) signal sequences of non-prokaryotic originfunction in prokaryotic cells and (2) different Fab-fusion proteins areexpressed from the same nucleic acid molecule in a host-cell dependentmanner when mRNA processing occurs in eukaryotic cells, but notprokaryotic cells (Fab-phage fusion proteins in prokaryotic cells andFab-Fc fusion proteins in eukaryotic cells). Accordingly, describedherein are nucleic acid molecules for the expression and secretion of aFab fragment fused to a phage particle protein, coat protein or adaptorprotein for phage display in bacteria when the nucleic acid istransformed into prokaryotic host cells (e.g. E. coli) and a Fabfragment fused to Fc when the nucleic acid is transformed intoeukaryotic cells (e.g. mammalian cells), without the need forsubcloning, and methods of use.

In one embodiment, the invention provides a nucleic acid moleculeencoding a first polypeptide comprising VH-HVR1, VH-HVR2 and HVR3 of avariable heavy chain domain (VH) and/or a second polypeptide comprisingVL-HVR1, VL-HVR2 and VL-HVR3 of a variable light chain domain, andwherein the nucleic acid molecule further encodes a signal sequencewhich is functional in both a prokaryotic and an eukaryotic cell and isencoded by a nucleic acid sequence that is operably linked to the firstand/or second polypeptide sequence, and wherein a full-length antibodyis expressed from the first and/or second polypeptide of the nucleicacid molecule. In another embodiment, the first and/or secondpolypeptide further comprises a variable heavy chain (VH) domain and avariable light chain (VL) domain. In a further embodiment, the VH domainis linked to CH1 and the VL domain is linked to CL.

In one aspect, the present invention provides a nucleic acid molecule,encoding VH-HVR1, VH-HVR2 and VH-HVR3 of a variable heavy chain domain(VH) and VL-HVR1, VL-HVR2 and VL-HVR3 of a variable light chain domain(VL) and comprising a prokaryotic promoter and an eukaryotic promoterwhich promoters are operably linked to the HVRs of the VH and/or theHVRS of the VL to allow for expression of the HVRs of the VH and theHVRs of the VL in a prokaryotic and a eukaryotic cell, and wherein theHVRs of the VH and/or VL is linked to a utility peptide when expressedby a eukaryotic cell and wherein the nucleic acid further encodes asignal sequence which is functional in both a prokaryotic and aneukaryotic cell.

In another aspect, the present invention provides a nucleic acidmolecule encoding a variable heavy chain (VH) domain and a variablelight chain (VL) domain and comprising a prokaryotic promoter and aneukaryotic promoter which promoters are operably linked to the VH domainand/or VL domain to allow for expression of a VH domain and/or a VLdomain in a prokaryotic and a eukaryotic cell, and wherein the VH domainand/or VL is linked to a utility peptide when expressed by a eukaryoticcell and wherein the nucleic acid further encodes a signal sequencewhich functions in both a prokaryotic and an eukaryotic cell.

In one embodiment, the VL and VH are linked to utility peptides. In afurther embodiment, the VH is further linked to a CH1 and the VL islinked to a CL. The utility peptide is selected from the groupconsisting of a Fc, tag, label and control protein. In one embodimentthe VL is linked to a control protein and the VH is linked to a Fc. Forexample, the control protein is a gD protein, or a fragment thereof.

In an even further embodiment the first and/or second polypeptide of theinvention is fused to a coat protein (e.g. pI, pII, pIII, pIV, pV, pVI,pVII, pVIII, pIX and pX of bacteriophage M13, f1 or fd, or a fragmentthereof such as amino acids 267-421 or 262-418 of the pIII protein(“pI”, “pII”, “pIII”, “pIV”, “pV”, “pVI”, “pVII”, “pVIII”, “pIX”, and“pX” when used herein refers to the full-length protein or fragmentsthereof unless specified otherwise)) or an adaptor protein (e.g. aleucine zipper protein or a polypeptide comprising an amino acidsequence of SEQ ID NO: 12 (cJUN(R): ASIARLEEKV KTLKAQNYEL ASTANMLREQVAQLGGC) or SEQ ID NO: 13 (FosW(E): ASIDELQAEV EQLEERNYAL RKEVEDLQKQAEKLGGC) or a variant thereof (amino acids in SEQ ID NO: 12 and SEQ IDNO: 13 that may be modified include, but are not limited to those thatare underlined and in bold), wherein the variant has an amino acidmodification wherein the modification maintains or increases theaffinity of the adaptor protein to another adaptor protein, or apolypeptide comprising the amino acid sequence selected from the groupconsisting of SEQ ID NO: 6 (ASIARLRERVKTLRARNYELRSRANMLRERVAQLGGC) orSEQ ID NO: 7 (ASLDELEAEIEQLEEENYALEKEIEDLEKELEKLGGC)) or a polypeptidecomprising an amino acid sequence of SEQ ID NO: 8 (GABA-R1: EEKSRLLEKENRELEKIIAE KEERVSELRH QLQSVGGC) or SEQ ID NO: 9 (GABA-R2: TSRLEGLQSENHRLRMKITE LDKDLEEVTM QLQDVGGC) or SEQ ID NO: 14 (Cys: AGSC) or SEQ IDNO: 15 (Hinge: CPPCPG). The nucleic acid molecule encoding for the coatprotein or adaptor protein is comprised within a synthetic intron. Thesynthetic intron is located between the nucleic acid encoding for the VHdomain and the nucleic acid encoding for the Fc. The synthetic intronfurther comprises nucleic acid encoding for a naturally occurring intronfrom IgG1 wherein the naturally occurring intron may selected from thegroup comprising intron 1, intron 2 or intron 3 from IgG1.

In one embodiment, the invention provides a nucleic acid molecule,wherein in prokaryotic cells, a first fusion protein is expressed and ineukaryotic cells, a second fusion protein is expressed. The first fusionprotein and the second fusion protein may be the same or different. In afurther embodiment, the first fusion protein may be a Fab-phage fusionprotein (e.g the Fab-phage fusion protein comprises VH/CH1 fused to thepIII) and the second fusion may be a Fab-Fc or Fab-hinge-Fc fusionprotein (e.g. the Fab-Fc or Fab-hinge-Fc fusion protein comprises VH/CH1fused to Fc).

In one embodiment, the invention provides a nucleic acid molecule,wherein the signal sequence directs protein secretion to the endoplasmicreticulum or outside of the cell in eukaryotic cells and/or wherein thesignal sequence directs protein secretion to the periplasm or outside ofthe cell in prokaryotic cells. Further, the signal sequence may beencoded by a nucleic acid sequence which encodes for the amino acidsequence comprising the amino acid sequence of SEQ ID NO: 10(XMKFTVVAAALLLLGAVRA, wherein X=0 amino acids or 1 or 2 amino acids(e.g. X=M (SEQ ID NO: 3; MMKFTVVAAALLLLGAVRA; wild-type mBIP) or X=MT(SEQ ID NO: 19; MTMKFTVVAAALLLLGAVRA) or X is absent (SEQ ID NO: 20;MKFTVVAAALLLLGAVRA) or by a nucleic acid sequence which encodes mBIP(SEQ ID NO: 4; ATG ATG AAA TTT ACC GTG GTG GCG GCG GCG CTG CTG CTG CTGGGC GCG GTC CGC GCG), and variants thereof, or by a nucleic acidsequence which encodes for an amino acid sequence having at least 90%amino acid sequence identity to an amino acid sequence selected from SEQID NO: 3 (mBIP amino acid sequence), and wherein the signal sequencefunctions in both prokaryotic and eukaryotic cells, or by the nucleicacid sequence of SEQ ID NO: 11 (consensus mBIP sequence, X ATG AAN TTNACN GTN GTN GCN GCN GCN CTN CTN CTN CTN GGN GCN GTN CGN GCN, whereinN=A, T, C or G, wherein X=ATG (SEQ ID NO: 5; ATG ATG AAN TTN ACN GTN GTNGCN GCN GCN CTN CTN CTN CTN GGN GCN GTN CGN GCN), X=ATG ACC (SEQ ID NO:21; ATG ACC ATG AAN TTN ACN GTN GTN GCN GCN GCN CTN CTN CTN CTN GGN GCNGTN CGN GCN) or X=is absent (SEQ ID NO: 22; ATG AAN TTN ACN GTN GTN GCNGCN GCN CTN CTN CTN CTN GGN GCN GTN CGN GCN), or by a nucleic acidsequence selected from the group of SEQ ID NO: 16 (mBIP.Opt1: ATG ATGAAA TTT ACC GTT GTT GCT GCT GCT CTG CTA CTT CTT GGA GCG GTC CGC GCA),SEQ ID NO: 17 (mBIP.Opt2: ATG ATG AAA TTT ACT GTT GTT GCG GCT GCT CTTCTC CTT CTT GGA GCG GTC CGC GCA) and SEQ ID NO: 18 (mBIP.Opt3: ATG ATGAAA TTT ACT GTT GTC GCT GCT GCT CTT CTA CTT CTT GGA GCG GTC CGC GCA).

In a further embodiment, the synthetic intron in the nucleic acidmolecule is flanked by nucleic acid encoding the CH1 at its 5′ end andnucleic acid encoding the Fc at its 3′ end. Further, the nucleic acidencoding the CH1 domain comprises a portion of the natural splice donorsequence and the nucleic acid encoding the Fc comprises a portion of thenatural splice acceptor sequence. Alternatively, the nucleic acidencoding the CH1 domain comprises a portion of a modified splice donorsequence wherein the modified splice donor sequence comprisesmodification of at least one nucleic acid residue and wherein themodification increases splicing.

In one embodiment, the prokaryotic promoter is phoA, Tac, Tphac or Lacpromoter and/or the eukaryotic promoter is CMV or SV40 or Moloney murineleukemia virus U3 region or caprine arthritis-encephalitis virus U3region or visna virus U3 region or retroviral U3 region sequence.Expression by the prokaryotic promoter occurs in a bacteria cell andexpression by a eukaryotic promoter occurs in a mammalian cell. In afurther embodiment, the bacteria cell is an E. coli cell and theeukaryotic cell is a yeast cell, CHO cell, 293 cell or NSO cell.

In another embodiment, the present invention provides a vectorcomprising the nucleic acid molecules described herein and/or a hostcell transformed with such vectors. The host cell may be a bacterialcell (e.g. an E. coli cell) or an eukaryotic cell (e.g. yeast cell, CHOcell, 293 cell or NSO cell).

In another embodiment, the present invention provides a process forproducing an antibody comprising culturing the host cell describedherein such that the nucleic acid is expressed. The process furthercomprises recovering the antibody expressed by the host cell and whereinthe antibody is recovered from the host cell culture medium.

In one aspect, the invention provides an adaptor protein comprising amodification of at least one residue of the amino acid sequence of SEQID NO: 8, 9, 12, 13, 14 or 15. In one embodiment, the amino acidsequence is selected from the group consisting of SEQ ID NO: 6(ASIARLRERVKTLRARNYELRSRANMLRERVAQLGGC) or SEQ ID NO: 7(ASLDELEAEIEQLEEENYALEKEIEDLEKELEKLGGC). In one embodiment, theinvention provides for nucleic acids encoding such adaptor proteins.

In one aspect, the invention provides a nucleic acid molecule encoding amBIP polypeptide comprising the amino acid sequence of SEQ ID NO: 3 orvariants thereof, which is functional in both prokaryotic and eukaryoticcells, or a polypeptide having an amino acid sequence with 85% homologywith the amino acid sequence of SEQ ID NO: 3. In one embodiment, theinvention provides a method of expressing a mBIP polypeptide comprisingthe amino acid sequence of SEQ ID NO: 3 or variants thereof in bothprokyarotic and eukaryotic cells. In one embodiment, the inventionprovides a bacterial cell that expresses a mBIP sequence comprising theamino acid sequence of SEQ ID NO: 3, or variants thereof.

In one aspect, the invention provides that the synthetic intron islocated between the nucleic acid encoding for the VH domain and thenucleic acid encoding for the Fc or the hinge of the antibody, betweenthe nucleic acid encoding for the CH2 and the CH3 domain of theantibody, between the nucleic acid encoding for the hinge region and theCH2 domain of the antibody.

In one aspect, the invention comprises a polypeptide comprising a signalsequence comprising the amino acid sequence of SEQ ID NO: 3, or variantsthereof, a variable heavy chain domain (VH) and a variable light chaindomain (VL) wherein the VH domain is connected to the N-terminus of theVL domain, or a polypeptide comprising a signal sequence comprising theamino acid sequence of SEQ ID NO: 3, or variants thereof, a variableheavy chain domain (VH) and a variable light chain domain (VL) whereinthe VH domain is connected to the C-terminus of the VL domain, or apolypeptide comprising a signal sequence comprising the amino acidsequence of SEQ ID NO: 3 and a VH-HVR1, VH-HVR2, and VH-HVR3 of avariable heavy chain domain (VH), or a polypeptide comprising a signalsequence comprising the amino acid sequence of SEQ ID NO: 3 and aVL-HVR1, VL-HVR2, and VL-HVR3 of a variable light chain domain (VL), ora polypeptide comprising a signal sequence comprising the amino acidsequence of SEQ ID NO: 3, or variants thereof, a VH-HVR1, VH-HVR2, andVH-HVR3 of a variable heavy chain domain (VH) and a VL-HVR1, VL-HVR2 andVL-HVR3 of a variable light chain domain (VL). In one embodiment, thepolypeptide of the invention is an antibody or antibody fragment. Theantibody or antibody fragment of the invention may be selected from thegroup consisting of F(ab′)2 and Fv fragments, diabodies, andsingle-chain antibody molecules.

In one aspect, the invention comprises a mutant helper phage forenhancing phage display of proteins. In one embodiment, the nucleotidesequence of a helper phage comprising an amber mutation in pIII whereinthe helper phage comprising an amber mutation enhances display ofproteins fused to pIII on phage. In a further embodiment, the nucleotidesequence of claim 70 wherein the amber mutation is a mutation innucleotides 2613, 2614 and 2616 of the nucleic acid for M13KO7. In aneven further embodiment, the nucleotide sequence of claim 71 wherein themutation in nucleotides 2613, 2614 and 2616 of the nucleic acid forM13KO7 introduces an amber stop codon.

BRIEF DESCRIPTION OF THE FIGURES

FIGS. 1A and 1B. (A) Her2 phage ELISA of purified phage displayinganti-Her2 Fab under the control of four different eukaryotic signalsequences (mBiP, Gaussia princeps, yBGL2, hGH). The heat-stableenterotoxin II (STII) prokaryotic signal sequence commonly used inphagemids serves as a benchmark. (B) Phage display of anti-Her2 Fabfused to wild-type eukaryotic mBiP signal sequence (mBiP.wt) and thecodon optimized versions obtained by phage library panning (mBiP.Opt1,mBiP.Opt2 and mBip.Opt3 (SEQ ID NOs: 16-18)).

FIGS. 2A and 2B. (A) Expression yields from 30 mL 293 cell suspensioncultures of individual clones and (B) aggregate statistics for hIgG1clones expressed as fusions to either the eukaryotic mBiP or theprokaryotic native IgG HC (VHS) signal sequence.

FIGS. 3A-3C. (A) Genomic structure of human IgG1 HC containing threenatural introns. Intron1 occurs immediately prior to the hinge region.(B) HC construct containing a synthetic intron derived from Intron1 or 3and containing a phage adaptor fusion peptide. The synthetic intron isflanked by the natural intron splice donor (D) and acceptor (A) fromIntron1 or 3. (C) HC construct containing a synthetic intron derivedfrom Intron1 or 3 and containing a phage coat fusion protein. Thesynthetic intron is flanked by the natural intron splice donor (D) andacceptor (A) from Intron1 or 3. Both Construct (B) and (C) contain aSTOP codon at the 3′ end of the adaptor peptide or phage coat proteinsequence.

FIGS. 4A and 4B. (A) Expression levels of h4D5 IgG from constructscontaining either no intron, a synthetic intron containing a phageadaptor peptide (See FIG. 3B), or a synthetic intron containing a phagecoat protein (gene-III, see FIG. 3C). (B) RT-PCR of hIgG1 HC fromtransfected cells. The predicted size for a properly-spliced HC mRNA is1,650 nt. The upper band in the adaptor+Intron1 construct represents anunspliced pre-cursor mRNA. The lower band in the adaptor- andgene-III-containing constructs is incorrectly spliced by a crypticsplice donor in the VH.

FIGS. 5A-5C. (A) Point mutations generated in the natural Intron1 splicedonor to increases conformity to the consensus splice donor formammalian mRNAs. (B) Optimization of the intron splice donor eliminatesthe accumulation of unspliced and incorrectly spliced HC mRNA and (C)increases expression in mammalian cells to the level observed when nointron is present

FIGS. 6A and 6B. (A) Modulation of display using pDV.5.0 and eitherwild-type KO7 (monovalent display) or adaptor KO7 (polyvalent display).(B) Expression of four different mAbs from pDV.5.0 in three differentmammalian cell lines.

FIG. 7 . Schematic of vector for expression and secretion ofpolypeptides in prokaryotic and eukaryotic cells. The synthetic intronmay contain either an adaptor sequence, or a phage coat protein sequencealong with any of the naturally-occurring introns sequences from hIgG1.Both the HC and LC may have either: 1) mammalian AND bacterial promotersupstream of the ORF, 2) a bacterial promoter ONLY upstream of the ORF(see also FIG. 14 ), or 3) a mammalian promoter only upstream of theORF. A construct in which both HC and LC have both promoter types isshown. The cassette containing gene-III with an adaptor peptide fusion(pDV5.0, shown) is only present when the synthetic intron contains anadaptor peptide fusion, but not when a phage coat protein fusion ispresent in the synthetic intron.

FIG. 8 . Nucleotide sequence of the pIII (nucleotides 1579 to 2853 (SEQID NO: 24)) of mutant helper phage Amber KO7 to enhance display ofproteins fused to pIII on M13 phage. Amber KO7 has an amber codonintroduced in the M13KO7 helper phage genome by site directedmutagenesis. The underlined residues are mutations in nucleotides 2613,2614 and 2616 (T2613C, C2614T and A2616G) that introduce an amber stop(TAG) in codon 346 and a silent mutation for an AvrII restriction sitein codon 345 of M13KO7 gene III. Nucleotide 1 of M13KO7 is the thirdresidue of the unique HpaI restriction site.

FIG. 9 . Enhanced display of Fab fragments on pIII of M13 phage by useof Amber KO7 helper phage. A conventional high-display phagemid withwild-type M13KO7 (open diamonds) drives levels of Fab displaysignificantly higher than those achieved by a low-display phagemidvector (closed squares) when wild-type M13KO7 is used for phageproduction. Use of a modified M13KO7 harboring an Amber mutation in pIII(Amber KO7) increases the display level of the low-display phagemid(closed triangles) to that of the high-display phagemid with wild-typeM13KO7 (open diamonds).

FIG. 10 is a bar graph which shows the binding (as measured by phageELISA) of clones selected from phage library sorting of a naïve dualvector Fab-phage library of Example 5 against immobilized VEGF.Individual clones were picked after four rounds of selection and phagesupernatants were tested for binding to immobilized antigen (VEGF) andto an irrelevant protein (Her2) to evaluate binding specificity.

FIG. 11 shows screening of selected phage clones in IgG format byBIAcore for antigen binding to VEGF, as measured by an Fc-capture assayon a BIAcore T100 instrument. The 96 clones that were picked forsequence analysis and phage ELISA were transfected into 293S cells (1mL) and cultured for seven days for IgG expression. Supernatants were0.2 μm filtered and used to evaluate VEGF antigen binding by anFc-capture assay on a BIAcore T100 instrument.

FIG. 12 shows the sequences of positive binders from the VEGF panningexperiment in Example 5. The heavy chain CDR sequence for eight clones(VEGF50 (SEQ ID NOS 25-27, respectively, in order of appearance), VEGF51(SEQ ID NOS 28-30, respectively, in order of appearance), VEGF 52 (SEQID NOS 31-33, respectively, in order of appearance), VEGF59 (SEQ ID NOS34-36, respectively, in order of appearance), VEGF55 (SEQ ID NOS 37-39,respectively, in order of appearance), VEGF60 (SEQ ID NOS 40-42,respectively, in order of appearance), VEGF61 (SEQ ID NOS 43-45,respectively, in order of appearance) and VEGF64 (SEQ ID NOS 46-48,respectively, in order of appearance)) is shown. All clones share thesame light chain CDR sequence.

FIG. 13 shows the ability of selected anti-VEGF IgGs selected from phagesorting against VEGF to inhibit binding of VEGF to one of its naturalreceptors, VEGF-R1. Selected antibodies from sorting against VEGF wereexpressed in CHO cells and purified IgG was used to measure the capacityof the selected clones to inhibit binding of VEGF to VEGF-R1. One clone(VEGF55) inhibited VEGF-R1 binding with an IC50 that was within 3.5-foldof bevacizumab (Avastin).

FIG. 14 shows a schematic of vector for expression and secretion ofpolypeptides in prokaryotic and eukaryotic cells, wherein the syntheticintron contains pIII, along with any of the naturally-occurring intronssequences from hIgG1 and wherein the LC has a bacterial promoterupstream of the ORF and the HC has both a mammalian and bacterialpromoter upstream of the ORF. Unlike the vector shown in FIG. 7 , thisvector (pDV6.5) does not require an additional gIII cassette for fusionto phage particles. The proteins resulting from expression in E. coliand mammalian cells are shown below the vector schematic. The dashedlines indicate introns in the heavy chain transcript spliced inmammalian cells. Note that part of the sequence encoding the IgG1 hingeis repeated in the vector to allow inclusion in both E. coli andmammalian cell expressed proteins.

FIG. 15 shows properties of full-length anti-VEGF IgGs expressed frompDV6.5. IgGs were expressed in 100 mL transfected CHO cell cultures andpurified by protein A chromatography. Final yields of purified IgG areindicated along with the score in a baculovirus ELISA used to measurenon-specific binding. The positive or negative binding of each clone inphage format (phage ELISA) or IgG format (BIAcore) is also indicated.

DETAILED DESCRIPTION OF EMBODIMENTS OF THE INVENTION I. Definitions

The term “synthetic intron” herein is used to define a segment ofnucleic acid that is situated between the nucleic acid encoding the CH1and the nucleic acid encoding the Hinge-Fc or The “synthetic intron” maybe any nucleic acid which does not encode for protein synthesis, anynucleic acid which does encode for protein synthesis, such as a phageparticle protein or coat protein (e.g pI, pII, pIII, pIV, pV, pVI, pVII,pVIII, pIX, pX), or an adaptor protein (e.g. a leucine-zipper, etc.), orany combination thereof. In one embodiment, the “synthetic intron”comprises part of a splice donor sequence and a splice acceptor sequencewhich allow a splice event. The splice donor and splice acceptorsequences allow the splice event and may comprise natural or syntheticnucleic acid sequences.

The term “utility polypeptide” herein is used to refer to a polypeptidethat is useful for a number of activities, such as useful for proteinpurification, protein tagging, protein labeling (e.g. labeling with adetectable compound or composition (e.g. radioactive label, fluorescentlabel or enzymatic label). A label may be indirectly conjugated with anamino acid side chain, an activated amino acid side chain, a cysteineengineered antibody, and the like. For example, the antibody can beconjugated with biotin and any of the three broad categories of labelsmentioned above can be conjugated with avidin or streptavidin, or viceversa. Biotin binds selectively to streptavidin and thus, the label canbe conjugated with the antibody in this indirect manner. Alternatively,to achieve indirect conjugation of the label with the polypeptidevariant, the polypeptide variant is conjugated with a small hapten(e.g., digoxin) and one of the different types of labels mentioned aboveis conjugated with an anti-hapten polypeptide variant (e.g.,anti-digoxin antibody). Thus, indirect conjugation of the label with thepolypeptide variant can be achieved (Hermanson, G. (1996) inBioconjugate Techniques Academic Press, San Diego).

Nucleic acid is “operably linked” when it is placed into a functionalrelationship with another nucleic acid sequence. For example, DNA for apresequence or secretory leader is operably linked to DNA for apolypeptide if it is expressed as a preprotein that participates in thesecretion of the polypeptide; a promoter or enhancer is operably linkedto a coding sequence if it affects the transcription of the sequence; ora ribosome binding site is operably linked to a coding sequence if it ispositioned so as to facilitate translation. Generally, “operably linked”means that the linked DNA sequences exist in a nucleic acid molecule insuch a way that they have a functional relationship with each other asnucleic acids or as proteins that are expressed by them. They may becontiguous or not. In the case of a secretory leader, they are oftencontiguous and in reading phase. However, enhancers do not have to becontiguous. Linking is accomplished by ligation at convenientrestriction sites. If such sites do not exist, the syntheticoligonucleotide adaptors or linkers can be used.

VH or VL domains are “linked” to a phage when the nucleic acid encodingthe heterologous protein sequence (for example, VH or VL domains) isinserted directly into the nucleic acid encoding a phage coat protein(for example, pII, pVI, pVII, pVIII or pIX). When introduced into aprokaryotic cell, a phage will be produced in which the coat protein candisplay the VH or VL domains. In one embodiment, the resulting phageparticles display antibody fragments fused to the amino or carboxytermini of phage coat proteins.

The terms “linked” or “links” or “link” as used herein are meant torefer to the covalent joining of two amino acids sequences or twonucleic acid sequences together through peptide or phosphodiester bonds,respectively, such joining can include any number of additional aminoacid or nucleic acid sequences between the two amino acid sequences ornucleic acid sequences that are being joined. For example, there can bea direct peptide bond linkage between a first and second amino acidsequence or a linkage that involves one or more amino acid sequencesbetween the first and second amino acid sequences.

By “linker” as used herein is meant an amino acid sequence of two ormore amino acids in length. The linker can consist of neutral polar ornonpolar amino acids. A linker can be, for example, 2 to 100 amino acidsin length, such as between 2 and 50 amino acids in length, for example,3, 5, 10, 15, 20, 25, 30, 35, 40, 45, or 50 amino acids in length. Alinker can be “cleavable,” for example, by auto-cleavage, or enzymaticor chemical cleavage. Cleavage sites in amino acid sequences and enzymesand chemicals that cleave at such sites are well known in the art andare also described herein.

The term “signal sequence functions” refers to the biological activityof a signal sequence directing secreted proteins to the ER (ineukaryotes) or periplasm (in prokaryotes) or outside of the cell.

A “control protein” as used herein refers to a protein sequence whoseexpression is measured to quantitate the level of display of the proteinsequence. For example, the protein sequence can be an “epitope tag” thatenables the VH or VL to be readily purified by affinity purificationusing an anti-tag antibody or another type of affinity matrix that bindsto the epitope tag. Examples of tag polypeptides and their respectiveantibodies that are suitable include: poly-histidine (poly-His) orpoly-histidine-glycine (poly-His-gly) tags; the flu HA tag polypeptideand its antibody 12CA5 [Field et al., Mol. Cell. Biol., 8:2159-2165(1988)]; the c-myc tag and the 8F9, 3C7, 6E10, G4, B7 and 9E10antibodies thereto [Evan et al., Molecular and Cellular Biology,5:3610-3616 (1985)]; and the Herpes Simplex virus glycoprotein D (gD)tag and its antibody [Paborsky et al., Protein Engineering, 3(6):547-553(1990)]. Other tag polypeptides include the Flag-peptide [Hopp et al.,BioTechnology, 6:1204-1210 (1988)]; the KT3 epitope peptide [Martin etal., Science, 255:192-194 (1992)]; an α-tubulin epitope peptide [Skinneret al., J. Biol. Chem., 266:15163-15166 (1991)]; and the T7 gene 10protein peptide tag [Lutz-Freyermuth et al., Proc. Natl. Acad. Sci. USA,87:6393-6397 (1990)].

A “coat protein” as used herein refers to any of the five capsidproteins that are components of phage particles, including pIII, pVI,pVII, pVIII and pIX. In one embodiment, the “coat protein” may be usedto display proteins or peptides (see Phage Display, A PracticalApproach, Oxford University Press, edited by Clackson and Lowman, 2004,p. 1-26). In one embodiment, a coat protein may be the pIII protein orsome variant, part and/or derivative thereof. For example, a C-terminalpart of the M13 bacteriophage pIII coat protein (cP3), such as asequence encoding the C-terminal residues 267-421 of protein III of M13phage may be used. In one embodiment, the pIII sequence comprises theamino acid sequence of SEQ ID NO: 1(AEDIEFASGGGSGAETVESCLAKPHTENSFTNVWKDDKTLDRYANYEGCLWNATGVVVCTGDETQCYGTWVPIGLAIPENEGGGSEGGGSEGGGSEGGGTKPPEYGDTPIPGYTYINPLDGTYPPGTEQNPANPNPSLEES QPLNTFMFQNNRFRNRQGALTVYTGTVTQGTDPVKTYYQYTPVSSKAMYDAYWNGKFRDCAFHSGFNEDPFVCEYQGQSSDLPQPPVNAGGGSGGGSGGGSEGGGSEGGGSEGGGSEGGGSGGGSGSGDFDYEKMANANKGAMTENADENALQSDAKGKLDSVATDYGAAIDGFIGDVSGLANGNGATGDFAGSNSQMAVGDGDNSPLMNNFRQYLPSLPQSVECRPFVFSAGKPYEFSIDCDKINLFRGVFAFLLYVATFMYVFSTFANILRNKES). In one embodiment, the pIII fragment comprises the aminoacid sequence of SEQ ID NO: 2(SGGGSGSGDFDYEKMANANKGAMTENADENALQSDAKGKLDSVATDYGAAIDGFIGDVSGLANGNGATGDFAGSNSQMAQVGDGDNSPLMNNFRQYLPSLPQSVECRPFVFGAGKPYEFSIDCDKINLFRGVFAFLLYVATFMYVFSTFANILRNKES).

An “adaptor protein” as used herein refers to a protein sequence thatspecifically interacts with another adaptor protein sequence insolution. In one embodiment, the “adaptor protein” comprises aheteromultimerization domain. In one embodiment, the adaptor protein isa cJUN protein or a Fos protein. In another embodiment, the adaptorprotein comprises the sequence of SEQ ID NO: 6(ASIARLRERVKTLRARNYELRSRANMLRERVAQLGGC) or SEQ ID NO: 7(ASLDELEAEIEQLEEENYALEKEIEDLEKELEKLGGC).

As used herein, “heteromultimerization domain” refers to alterations oradditions to a biological molecule so as to promote heteromultimerformation and hinder homomultimer formation. Any heterodimerizationdomain having a strong preference for forming heterodimers overhomodimers is within the scope of the invention. Illustrative examplesinclude but are not limited to, for example, US Patent Application20030078385 (Arathoon et al.—Genentech; describing knob into holes);WO2007147901 (Kjergaard et al.—Novo Nordisk: describing ionicinteractions); WO 2009089004 (Kannan et al.—Amgen: describingelectrostatic steering effects); WO2011/034605 (Christensen etal.—Genentech; describing coiled coils). See also, for example, Pack, P.& Plueckthun, A., Biochemistry 31, 1579-1584 (1992) describing leucinezipper or Pack et al., Bio/Technology 11, 1271-1277 (1993) describingthe helix-turn-helix motif. The phrase “heteromultimerization domain”and “heterodimerization domain” are used interchangeably herein.

The term “Fab-fusion protein” is used herein to refer to a Fab-phagefusion protein in prokaryotic cells and/or a Fab-Fc fusion protein ineukaryotic cells. The Fab-Fc fusion may also be a Fab-hinge-Fc fusion.

The term “antibody” herein is used in the broadest sense and encompassesvarious antibody structures, including but not limited to monoclonalantibodies, polyclonal antibodies, multispecific antibodies (e.g.,bispecific antibodies), and antibody fragments so long as they exhibitthe desired antigen-binding activity.

An “antibody fragment” refers to a molecule other than an intactantibody that comprises a portion of an intact antibody that binds theantigen to which the intact antibody binds. Examples of antibodyfragments include but are not limited to Fv, Fab, Fab′, Fab′-SH,F(ab′)₂; diabodies; linear antibodies; single-chain antibody molecules(e.g. scFv); and multispecific antibodies formed from antibodyfragments.

The “class” of an antibody refers to the type of constant domain orconstant region possessed by its heavy chain. There are five majorclasses of antibodies: IgA, IgD, IgE, IgG, and IgM, and several of thesemay be further divided into subclasses (isotypes), e.g., IgG₁, IgG₂,IgG₃, IgG₄, IgA₁, and IgA₂. The heavy chain constant domains thatcorrespond to the different classes of immunoglobulins are called α, δ,ε, γ, and μ, respectively.

The term “Fe region” herein is used to define a C-terminal region of animmunoglobulin heavy chain that contains at least a portion of theconstant region. The term includes native sequence Fc regions andvariant Fc regions. In one embodiment, a human IgG heavy chain Fc regionextends from Cys226, or from Pro230, to the carboxyl-terminus of theheavy chain. However, the C-terminal lysine (Lys447) of the Fc regionmay or may not be present. Unless otherwise specified herein, numberingof amino acid residues in the Fc region or constant region is accordingto the EU numbering system, also called the EU index, as described inKabat et al., Sequences of Proteins of Immunological Interest, 5th Ed.Public Health Service, National Institutes of Health, Bethesda, M D,1991.

“Framework” or “FR” refers to variable domain residues other thanhypervariable region (HVR) residues. The FR of a variable domaingenerally consists of four FR domains: FR1, FR2, FR3, and FR4.Accordingly, the HVR and FR sequences generally appear in the followingsequence in VH (or VL): FR1-H1(L1)-FR2-H2(L2)-FR3-H3(L3)-FR4.

The terms “full length antibody,” “intact antibody,” and “wholeantibody” are used herein interchangeably to refer to an antibody havinga structure substantially similar to a native antibody structure orhaving heavy chains that contain an Fc region as defined herein.

The terms “host cell,” “host cell line,” and “host cell culture” areused interchangeably and refer to cells into which exogenous nucleicacid has been introduced, including the progeny of such cells. Hostcells include “transformants” and “transformed cells,” which include theprimary transformed cell and progeny derived therefrom without regard tothe number of passages. Progeny may not be completely identical innucleic acid content to a parent cell, but may contain mutations. Mutantprogeny that have the same function or biological activity as screenedor selected for in the originally transformed cell are included herein.

The term “hypervariable region” or “HVR,” as used herein, refers to eachof the regions of an antibody variable domain which are hypervariable insequence and/or form structurally defined loops (“hypervariable loops”).Generally, native four-chain antibodies comprise six HVRs; three in theVH (H1, H2, H3), and three in the VL (L1, L2, L3). HVRs generallycomprise amino acid residues from the hypervariable loops and/or fromthe “complementarity determining regions” (CDRs), the latter being ofhighest sequence variability and/or involved in antigen recognition.Exemplary hypervariable loops occur at amino acid residues 26-32 (L1),50-52 (L2), 91-96 (L3), 26-32 (HI), 53-55 (H2), and 96-101 (H3).(Chothia and Lesk, J. Mol. Biol. 196:901-917 (1987).) Exemplary CDRs(CDR-L1, CDR-L2, CDR-L3, CDR-H1, CDR-H2, and CDR-H3) occur at amino acidresidues 24-34 of L1, 50-56 of L2, 89-97 of L3, 31-35B of H1, 50-65 ofH2, and 95-102 of H3. (Kabat et al., Sequences of Proteins ofImmunological Interest, 5th Ed. Public Health Service, NationalInstitutes of Health, Bethesda, MD (1991).)

With the exception of CDR1 in VH, CDRs generally comprise the amino acidresidues that form the hypervariable loops. CDRs also comprise“specificity determining residues,” or “SDRs,” which are residues thatcontact antigen. SDRs are contained within regions of the CDRs calledabbreviated-CDRs, or a-CDRs. Exemplary a-CDRs (a-CDR-L1, a-CDR-L2,a-CDR-L3, a-CDR-H1, a-CDR-H2, and a-CDR-H3) occur at amino acid residues31-34 of L1, 50-55 of L2, 89-96 of L3, 31-35B of H1, 50-58 of H2, and95-102 of H3. (See Almagro and Fransson, Front. Biosci. 13:1619-1633(2008).) Unless otherwise indicated, HVR residues and other residues inthe variable domain (e.g., FR residues) are numbered herein according toKabat et al., supra.

An “individual” or “subject” is a mammal. Mammals include, but are notlimited to, domesticated animals (e.g., cows, sheep, cats, dogs, andhorses), primates (e.g., humans and non human primates such as monkeys),rabbits, and rodents (e.g., mice and rats). In certain embodiments, theindividual or subject is a human.

An “isolated” antibody is one which has been separated from a componentof its natural environment. In some embodiments, an antibody is purifiedto greater than 95% or 99% purity as determined by, for example,electrophoretic (e.g., SDS-PAGE, isoelectric focusing (IEF), capillaryelectrophoresis) or chromatographic (e.g., ion exchange or reverse phaseHPLC). For review of methods for assessment of antibody purity, see,e.g., Flatman et al., J. Chromatogr. B 848:79-87 (2007).

An “isolated” nucleic acid refers to a nucleic acid molecule that hasbeen separated from a component of its natural environment. An isolatednucleic acid includes a nucleic acid molecule contained in cells thatordinarily contain the nucleic acid molecule, but the nucleic acidmolecule is present extrachromosomally or at a chromosomal location thatis different from its natural chromosomal location.

“Isolated nucleic acid encoding an antibody” refers to one or morenucleic acid molecules encoding antibody heavy and light chains (orfragments thereof), including such nucleic acid molecule(s) in a singlevector or separate vectors, and such nucleic acid molecule(s) present atone or more locations in a host cell.

The term “monoclonal antibody” as used herein refers to an antibodyobtained from a population of substantially homogeneous antibodies,i.e., the individual antibodies comprising the population are identicaland/or bind the same epitope, except for possible variant antibodies,e.g., containing naturally occurring mutations or arising duringproduction of a monoclonal antibody preparation, such variants generallybeing present in minor amounts. In contrast to polyclonal antibodypreparations, which typically include different antibodies directedagainst different determinants (epitopes), each monoclonal antibody of amonoclonal antibody preparation is directed against a single determinanton an antigen. Thus, the modifier “monoclonal” indicates the characterof the antibody as being obtained from a substantially homogeneouspopulation of antibodies, and is not to be construed as requiringproduction of the antibody by any particular method. For example, themonoclonal antibodies to be used in accordance with the presentinvention may be made by a variety of techniques, including but notlimited to the hybridoma method, recombinant DNA methods, phage-displaymethods, and methods utilizing transgenic animals containing all or partof the human immunoglobulin loci, such methods and other exemplarymethods for making monoclonal antibodies being described herein.

A “naked antibody” refers to an antibody that is not conjugated to aheterologous moiety (e.g., a cytotoxic moiety) or radiolabel. The nakedantibody may be present in a pharmaceutical formulation.

“Native antibodies” refer to naturally occurring immunoglobulinmolecules with varying structures. For example, native IgG antibodiesare heterotetrameric glycoproteins of about 150,000 daltons, composed oftwo identical light chains and two identical heavy chains that aredisulfide-bonded. From N- to C-terminus, each heavy chain has a variableregion (VH), also called a variable heavy domain or a heavy chainvariable domain, followed by three constant domains (CH1, CH2, and CH3).Similarly, from N- to C-terminus, each light chain has a variable region(VL), also called a variable light domain or a light chain variabledomain, followed by a constant light (CL) domain. The light chain of anantibody may be assigned to one of two types, called kappa (κ) andlambda (λ), based on the amino acid sequence of its constant domain.

The term “package insert” is used to refer to instructions customarilyincluded in commercial packages of therapeutic products, that containinformation about the indications, usage, dosage, administration,combination therapy, contraindications and/or warnings concerning theuse of such therapeutic products.

The term “variable region” or “variable domain” refers to the domain ofan antibody heavy or light chain that is involved in binding theantibody to antigen. The variable domains of the heavy chain and lightchain (VH and VL, respectively) of a native antibody generally havesimilar structures, with each domain comprising four conserved frameworkregions (FRs) and three hypervariable regions (HVRs). (See, e.g., Kindtet al. Kuby Immunology, 6^(th) ed., W.H. Freeman and Co., page 91(2007).) A single VH or VL domain may be sufficient to conferantigen-binding specificity. Furthermore, antibodies that bind aparticular antigen may be isolated using a VH or VL domain from anantibody that binds the antigen to screen a library of complementary VLor VH domains, respectively. See, e.g., Portolano et al., J. Immunol.150:880-887 (1993); Clarkson et al., Nature 352:624-628 (1991).

The term “vector,” as used herein, refers to a nucleic acid moleculecapable of propagating another nucleic acid to which it is linked. Theterm includes the vector as a self-replicating nucleic acid structure aswell as the vector incorporated into the genome of a host cell intowhich it has been introduced. Certain vectors are capable of directingthe expression of nucleic acids to which they are operatively linked.Such vectors are referred to herein as “expression vectors.”

II. Detailed Description

The phage-based antibody discovery process utilizes phage displaytechnology to select Fab fragments with desired binding specificitiesfrom large pools of individual phage clones¹⁻³. In this approach, phagelibraries comprised of Fab fragments fused to M13 filamentous phageparticles, either directly or indirectly through one of the major coatproteins and containing diversified complementarity determining regions(CDRs), are generated using established molecular biology techniques andspecialized phage display vectors (Tohidkia et al., Journal of drugtargeting, 20: 195-208 (2012); Bradbury et al., Nature biotechnology,29: 245-254 (2011); Qi et al., Journal of molecular biology, 417:129-143 (2012)). While the theoretical diversity of such libraries caneasily exceed 10²⁵ unique sequences, practical limitations in theconstruction of phage pools typically constrains the actual diversity to≤10 ¹¹ clones for a given library (Sidhu et al., Methods in enzymology,328: 333-363 (2000)).

Given the substantial number of unique sequences that a starting librarymay contain, the screening throughput of selected clones is of criticalimportance. For phage-based antibody discovery, a thorough evaluation ofselected Fabs and the properties of their cognate full-length IgGs infunctional assays (target binding, cell-based activity assays, in vivohalf-life, etc.) requires reformatting of the Fab heavy chain (HC) andlight chain (LC) sequences into a full-length IgG by subcloning the DNAsequences encoding the HC and LC out of the phagemid vector used fordisplay and into mammalian expression vectors for IgG expression. Thelaborious process of subcloning dozens or hundreds of selected HC/LCpairs represents a major bottleneck in the phage-based antibodydiscovery process. Furthermore, since a substantial percentage ofselected Fabs, once reformatted, fail to perform satisfactorily ininitial screening assays, increasing the number of clones carriedthrough this reformatting/screening process greatly increases theultimate probability of success.

Here, we describe the generation of an expression and secretion systemfor the expression and secretion of one Fab fusion protein inprokaryotic cells and a distinct (or identical) Fab fusion in eukaryoticcells. For example, the expression and secretion system drivesexpression of a Fab-phage fusion when transformed into E. coli, anddrives expression of a full-length IgG bearing the same Fab fragmentwhen transfected into mammalian cells. We demonstrate that a mammaliansignal sequence from the murine binding immunoglobulin protein(mBiP)^(8,9) can drive efficient protein expression in both prokaryoticand eukaryotic cells. Using mammalian mRNA splicing to remove asynthetic intron containing a phage fusion peptide inserted within thehinge region of the human IgG₁ HC, we are able to generate two distinctproteins in a host cell-dependent fashion: a Fab fragment fused to anadaptor peptide for phage display in E. coli and native human IgG₁ inmammalian cells. This technology allows for the selection of Fabfragments that bind to an antigen of interest from a phage displaylibrary with subsequent expression and purification of the cognatefull-length IgGs in mammalian cells without the need for subcloning.

The invention is based, in part, on experimental findings demonstratingthat (1) signal sequences of non-bacterial origin function inprokaryotic cells at levels sufficient for sorting of phage librarieswithout compromising IgG expression in eukaryotic cells, and (2)different Fab-fusion proteins are expressed from the same nucleic acidmolecule in a host-cell dependent manner when mRNA processing occurs ineukaryotic cells, but not prokaryotic cells (Fab-phage fusion proteinsin prokaryotic cells and Fab-Fc fusion proteins in eukaryotic cells).Accordingly, described herein is an expression and secretion system forthe expression and secretion of a Fab fragment fused to a phage particleprotein, coat protein or adaptor protein for phage display inprokaryotic host cells (e.g. E. coli) and a Fab fragment fused to Fc ineukaryotic cells (e.g. mammalian cells), without the need forsubcloning, and methods relating to the construction and use of theexpression and secretion system. In particular, vectors for expressionand secretion of a Fab-phage fusion protein in prokaryotic cells and aFab-Fc fusion protein in eukaryotic cells, nucleic acid molecules forexpression and secretion or proteins or peptides in prokaryotic andeukaryotic cells, and host cells comprising such vectors are describedherein. Further, methods of use of the expression and secretion system,including methods of use of the expression and secretion system forscreening and selection of novel antibodies against proteins ofinterest, is described herein.

MODES OF CARRYING OUT THE INVENTION

The practice of the present invention will employ, unless otherwiseindicated, conventional techniques of molecular biology (includingrecombinant techniques), microbiology, cell biology, biochemistry andimmunology, which are within the skill of the art. Such techniques areexplained fully in the literature, such as, “Molecular Cloning: ALaboratory Manual”, 2^(nd) edition (Sambrook et al., 1989);“Oligonucleotide Synthesis” (M. J. Gait, ed., 1984); “Animal CellCulture” (R. I. Freshney, ed., 1987); “Methods in Enzymology” (AcademicPress, Inc.); “Handbook of Experimental Immunology”, 4^(th) edition (D.M. Weir & C. C. Blackwell, eds., Blackwell Science Inc., 1987); “GeneTransfer Vectors for Mammalian Cells” (J. M. Miller & M. P. Calos, eds.,1987); “Current Protocols in Molecular Biology” (F. M. Ausubel et al.,eds., 1987); “PCR: The Polymerase Chain Reaction”, (Mullis et al., eds.,1994); and “Current Protocols in Immunology” (J. E. Coligan et al.,eds., 1991).

Expression and Secretion System for Prokaryotic and Eukaryotic Cells

The expression and secretion system for prokaryotic and eukaryotic cellsinvolves a vector which contains the regulatory and coding sequences fora protein of interest (e.g. the heavy or light chains of an IgGmolecule), wherein prokaryotic and eukaryotic promoters (e.g. CMV(eukaryotic) and PhoA (prokaryotic)) are arranged in tandem upstream ofthe gene(s) of interest, and a single signal sequences drives theexpression of the protein of interest in prokaryotic and eukaryoticcells. The present invention provides a means for this vector togenerate two different fusion forms of the protein of interest in ahost-cell dependent manner by using a synthetic intron located betweenthe VH/CH1 and the hinge-Fc region of IgG1 wherein the synthetic intronis spliced out during mRNA processing in eukaryotic cells.

A. Signal Sequence that Functions in Both Prokaryotic and EukaryoticCells

One challenge in constructing a vector capable of expressing proteins ofinterest in both prokaryotic (E. coli) and eukaryotic (mammalian) cellsarises from differences in signal sequences found in these cell types.While certain features of signal sequences are generally conserved inboth prokaryotic and eukaryotic cells (e.g. a patch of hydrophobicresidues located in the middle of the sequence and polar/chargedresidues adjacent to the cleavage site at the N-terminus of the maturepolypeptide), others are more characteristic of one cell type than theother. Moreover, it is known in the art that different signal sequencescan have significant impact on expression levels in mammalian cells,even if the sequences are all of mammalian origin (Hall et al., J ofBiological Chemistry, 265: 19996-19999 (1990); Humphreys et al., ProteinExpression and Purification, 20: 252-264 (2000)). For instance,bacterial signal sequences typically have positively-charged residues(most commonly lysine) directly following the initiating methionine,whereas these are not always present in mammalian signal sequences.While there are known signal sequences capable of directing secretion inboth cell types, such signal sequences typically direct high levels ofprotein secretion in only one cell type or the other.

While bacterial signal sequences have very rarely been shown to exhibitany functionality in mammalian cells, there have been reports of signalsequences of mammalian origin being capable of driving translocationinto the periplasm of bacteria (Humphreys et al., The Protein Expressionand Purification, 20: 252-264 (2000)). However, mere functionality ofthe signal sequence is not adequate for a robust dual expression systemto be used for phage display and IgG expression. Rather, the selectedsignal sequence must function well in both expression systems,particularly for phage display where low levels of display wouldcompromise the ability of the system to perform phage panningexperiments.

The present invention is based in part on the discovery that signalsequences of non bacterial origin function in prokaryotic cells atlevels sufficient for sorting of phage libraries without compromisingIgG expression in eukaryotic cells.

The present invention provides any signal sequence (including concensussignal sequences) which targets the polypeptide of interest to theperiplasm in prokaryotes and to the endoplasmic/reticulum in eukaryotes,may be used. Signal sequences that may be used include but are notlimited to the murine binding immunoglobulin protein (mBiP) signalsequence (UniProtKB: accession P20029), signal sequences from humangrowth hormone (hGH) (UniProtKB: accession BIA4G6), Gaussia princepsluciferase (UniProtKB: accession Q9BLZ2), yeast endo-1,3-glucanase(yBGL2) (UniProtKB: accession P15703). In one embodiment, the signalsequence is a natural or synthetic signal sequence. In a furtherembodiment, the synthetic signal sequence is an optimized signalsecretion sequence that drives levels of display at an optimized levelcompared to its non-optimized natural signal sequence.

A suitable assay for determining the ability of signal sequences todrive display of polypeptides of interest in prokaryotic cells,includes, for example, phage ELISA, as described herein.

A suitable assay for determining the ability of signal sequences todrive expression of polypeptides of interest in eukaryotic cells,includes, for example, transfection of mammalian expression vectorsencoding the polypeptides of interest with the signal of interest intocultured mammalian cells, growing the cells for a period of time,collecting the supernatants from the cultured cells, and purifying IgGfrom the supernatants by affinity chromatography, as described herein.

B. Synthetic Intron that Results in Expression of Host-Dependent FusionProteins from the Same Nucleic Acid

The present invention is based in part on the discovery that differentFab-fusion proteins may be expressed from the same nucleic acid moleculein a host cell dependent manner by exploiting the natural process ofintron splicing which occurs during mRNA processing in eukaryotic, butnot prokaryotic cells.

The genomic sequence of hIgG1 HC constant region contains three naturalintrons (FIG. 3A), Intron 1, Intron 2 and Intron 3. Intron 1 is a 391base pair intron positioned between the HC variable domain/CH1 (VH/CH1)and the hinge region. Intron 2 is a 118 base pair intron positionedbetween the hinge region and CH2. Intron 3 is a 97 base pair intronpositioned between CH2 and CH3.

The present invention provides a vector which comprises Intron 1positioned between the VH/CH1 and hinge region. Other examples, includeIntron 2 or Intron 3 positioned between the VH/CH1 and hinge region. Forsome vectors, nucleic acid encoding for a coat protein ro an adaptorprotein are inserted into the intron positioned between VH/CH1 and thehinge region with the natural plice donor for the intron at its 5′ endand the natural splice acceptor at its 3′ end.

Other examples, include a mutant splice donor with substitutions atpositions 1 and 5 out of 8 positions of the splice donor.

For example, phage ELISA may be used to analyze the expression andsecretion system in prokaryotic cells.

For example, purification of IgG from culture supernatants using proteinA and gel filtration chromatography may be used to analyze theexpression and secretion system in eukaryotic cells. Further, RT-PCR maybe used to analyze the splicing of the synthetic intron-containing HCcassette in eukaryotic cells.

C. Vector for Expression and Secretion of Polypeptides in Prokarytoicand Eukaryotic Cells

The expression and secretion system for expression and secretion ofFab-fusion proteins in prokaryotic and eukaryotic cells may beconstructed using a variety of techniques which are within the skill ofthe art.

In one aspect, the expression and secretion system comprises a vectorcomprising: (1) a mammalian promoter, (2) LC cassette, comprising (inorder from 5′ to 3′) a bacterial promoter, a signal sequence, anantibody light chain sequence, a control protein (gD); (3) syntheticcassette comprising (in order from 5′ to 3′) a mammalianpolyadenylation/transcriptional stop signal, a transcriptionalterminator sequence for halting transcription in prokaryotic cells, amammalian promoter and a bacterial promoter for driving expression ofthe HC; (4) HC cassette, comprising a signal sequence and an antibodyheavy chain sequence; and (5) second synthetic cassette comprising amammalian polyadenylation/transcriptional stop signal and atranscriptional terminator sequence for halting transcription inprokaryotic cells. The secretional signal sequence preceding the LC andHC may be the same signal sequence that functions in both prokaryoticand eukaryotic cells (e.g. the mammalian mBiP signal sequence). In oneembodiment, the antibody heavy chain sequence comprises a syntheticintron. The synthetic intron is positioned with the VH/CH1 domain (atits 5′ end) and the hinge region (at its 3′ end). In one embodiment, thesynthetic intron is flanked by an optimized splice donor sequence at the5′ end and the natural intron 1 splice acceptor sequence at the 3′ end.In one embodiment, the synthetic intron comprises a nucleotide sequencewhich encodes for a phage coat protein (e.g. pIII) for direct fusiondisplay (see FIG. 14 ), or an adaptor protein fused at the nucleotidelevel to intron 1 for indirect fusion display (see FIG. 7 ). Forindirect fusion display, the vector further comprises a separatebacterial expression cassette comprising (in order from 5′ to 3′)bacterial promoter, a bacterial signal sequence, a phage coat protein(e.g. pIII) with a partner adaptor peptide fused at the nucleotide levelto the N-terminus of the coat protein and a transcriptional terminatorsequence (see FIG. 7 ). In addition, different embodiments of the aboveconstructs are possible in which both the HC and LC are controlled by amammalian and bacterial promoter in tandem (see FIG. 7 ) or only one(e.g., HC) cassette is controlled by tandem mammalian and bacterialpromoters whereas the other (e.g., LC) cassette is controlled only by abacterial promoter (see FIG. 14 ).

Further, the vector includes a bacterial origin of replication, amammalian origin of replication, nucleic acid which encodes forpolypeptides useful as a control (e.g. gD protein) or useful foractivities such as a protein purification, protein tagging, proteinlabeling (e.g. labeling with a detectable compound or composition (e.g.radioactive label, fluorescent label or enzymatic label).

In one embodiment, the mammalian and bacterial promoters and signalsequences are operably linked to the antibody light chain sequence andmammalian and bacterial promoters and signal sequences are operablylinked to the antibody heavy chain sequence.

D. Selection and Screening of Antibodies Against Antigens of Interest

The present invention provides a method of screening and selectingantibodies against proteins of interest by phage or bacterial display ofFab-based libraries or to optimize existing antibodies by similarmethods. Use of the dual vector described above may be used forscreening and selecting of Fab fragments in prokaryotic cells, and theselection of Fabs that can be readily expressed as full-length IgGmolecules for further testing without the need for subcloning.

Antibodies of Invention

In a further aspect of the invention, an antibody according to any ofthe above embodiments is a monoclonal antibody, including a chimeric,humanized or human antibody. In one embodiment, an antibody is anantibody fragment, e.g., a Fv, Fab, Fab′, scFv, diabody, or F(ab′)₂fragment. In another embodiment, the antibody is a full length antibody,e.g., an intact IgG1, IgG2, IgG3 or IgG4 antibody or other antibodyclass or isotype as defined herein.

In a further aspect, an antibody according to any of the aboveembodiments may incorporate any of the features, singly or incombination, as described in Sections 1-7 below:

I. Antibody Affinity

In certain embodiments, an antibody provided herein has a dissociationconstant (Kd) of ≤1 μM, ≤100 nM, ≤10 nM, ≤1 nM, ≤0.1 nM, ≤0.01 nM, or≤0.001 nM (e.g. 10⁻⁸M or less, e.g. from 10⁻⁸M to 10⁻¹³M, e.g., from10⁻⁹M to 10⁻¹³ M).

In one embodiment, Kd is measured by a radiolabeled antigen bindingassay (RIA) performed with the Fab version of an antibody of interestand its antigen as described by the following assay. Solution bindingaffinity of Fabs for antigen is measured by equilibrating Fab with aminimal concentration of (¹²⁵I)-labeled antigen in the presence of atitration series of unlabeled antigen, then capturing bound antigen withan anti-Fab antibody-coated plate (see, e.g., Chen et al., J. Mol. Biol.293:865-881(1999)). To establish conditions for the assay, MICROTITER®multi-well plates (Thermo Scientific) are coated overnight with 5 μg/mlof a capturing anti-Fab antibody (Cappel Labs) in 50 mM sodium carbonate(pH 9.6), and subsequently blocked with 2% (w/v) bovine serum albumin inPBS for two to five hours at room temperature (approximately 23° C.). Ina non-adsorbent plate (Nunc #269620), 100 pM or 26 pM [¹²⁵I]-antigen aremixed with serial dilutions of a Fab of interest (e.g., consistent withassessment of the anti-VEGF antibody, Fab-12, in Presta et al., CancerRes. 57:4593-4599 (1997)). The Fab of interest is then incubatedovernight; however, the incubation may continue for a longer period(e.g., about 65 hours) to ensure that equilibrium is reached.Thereafter, the mixtures are transferred to the capture plate forincubation at room temperature (e.g., for one hour). The solution isthen removed and the plate washed eight times with 0.1% polysorbate 20(TWEEN-20®) in PBS. When the plates have dried, 150 μl/well ofscintillant (MICROSCINT-20 T_(M); Packard) is added, and the plates arecounted on a TOPCOUNT T_(M) gamma counter (Packard) for ten minutes.Concentrations of each Fab that give less than or equal to 20% ofmaximal binding are chosen for use in competitive binding assays.

According to another embodiment, Kd is measured using surface plasmonresonance assays using a BIACORE®-2000 or a BIACORE®-3000 (BIAcore,Inc., Piscataway, NJ) at 25° C. with immobilized antigen CM5 chips at˜10 response units (RU). Briefly, carboxymethylated dextran biosensorchips (CM5, BIACORE, Inc.) are activated withN-ethyl-N′-(3-dimethylaminopropyl)-carbodiimide hydrochloride (EDC) andN-hydroxysuccinimide (NHS) according to the supplier's instructions.Antigen is diluted with 10 mM sodium acetate, pH 4.8, to 5 μg/ml (˜0.2μM) before injection at a flow rate of 5 μl/minute to achieveapproximately 10 response units (RU) of coupled protein. Following theinjection of antigen, 1 M ethanolamine is injected to block unreactedgroups. For kinetics measurements, two-fold serial dilutions of Fab(0.78 nM to 500 nM) are injected in PBS with 0.05% polysorbate 20(TWEEN-20™) surfactant (PBST) at 25° C. at a flow rate of approximately25 μl/min. Association rates (k_(on)) and dissociation rates (k_(off))are calculated using a simple one-to-one Langmuir binding model(BIACORE® Evaluation Software version 3.2) by simultaneously fitting theassociation and dissociation sensorgrams. The equilibrium dissociationconstant (Kd) is calculated as the ratio k_(off)/k_(on). See, e.g., Chenet al., J. Mol. Biol. 293:865-881 (1999). If the on-rate exceeds 10⁶M⁻¹s⁻¹ by the surface plasmon resonance assay above, then the on-ratecan be determined by using a fluorescent quenching technique thatmeasures the increase or decrease in fluorescence emission intensity(excitation=295 nm; emission=340 nm, 16 nm band-pass) at 25° C. of a 20nM anti-antigen antibody (Fab form) in PBS, pH 7.2, in the presence ofincreasing concentrations of antigen as measured in a spectrometer, suchas a stop-flow equipped spectrophometer (Aviv Instruments) or a8000-series SLM-AMINCO™ spectrophotometer (ThermoSpectronic) with astirred cuvette.

2. Antibody Fragments

In certain embodiments, an antibody provided herein is an antibodyfragment. Antibody fragments include, but are not limited to, Fab, Fab′,Fab′-SH, F(ab′)₂, Fv, and scFv fragments, and other fragments describedbelow. For a review of certain antibody fragments, see Hudson et al.Nat. Med. 9:129-134 (2003). For a review of scFv fragments, see, e.g.,Pluckthün, in The Pharmacology of Monoclonal Antibodies, vol. 113,Rosenburg and Moore eds., (Springer-Verlag, New York), pp. 269-315(1994); see also WO 93/16185; and U.S. Pat. Nos. 5,571,894 and5,587,458. For discussion of Fab and F(ab′)₂ fragments comprisingsalvage receptor binding epitope residues and having increased in vivohalf-life, see U.S. Pat. No. 5,869,046.

Diabodies are antibody fragments with two antigen-binding sites that maybe bivalent or bispecific. See, for example, EP 404,097; WO 1993/01161;Hudson et al., Nat. Med. 9:129-134 (2003); and Hollinger et al., Proc.Natl. Acad. Sci. USA 90: 6444-6448 (1993). Triabodies and tetrabodiesare also described in Hudson et al., Nat. Med. 9:129-134 (2003).

Single-domain antibodies are antibody fragments comprising all or aportion of the heavy chain variable domain or all or a portion of thelight chain variable domain of an antibody. In certain embodiments, asingle-domain antibody is a human single-domain antibody (Domantis,Inc., Waltham, MA; see, e.g., U.S. Pat. No. 6,248,516 B1).

Antibody fragments can be made by various techniques, including but notlimited to proteolytic digestion of an intact antibody as well asproduction by recombinant host cells (e.g. E. coli or phage), asdescribed herein.

3. Chimeric and Humanized Antibodies

In certain embodiments, an antibody provided herein is a chimericantibody. Certain chimeric antibodies are described, e.g., in U.S. Pat.No. 4,816,567; and Morrison et al., Proc. Natl. Acad. Sci. USA,81:6851-6855 (1984)). In one example, a chimeric antibody comprises anon-human variable region (e.g., a variable region derived from a mouse,rat, hamster, rabbit, or non-human primate, such as a monkey) and ahuman constant region. In a further example, a chimeric antibody is a“class switched” antibody in which the class or subclass has beenchanged from that of the parent antibody. Chimeric antibodies includeantigen-binding fragments thereof.

In certain embodiments, a chimeric antibody is a humanized antibody.Typically, a non human antibody is humanized to reduce immunogenicity tohumans, while retaining the specificity and affinity of the parentalnon-human antibody. Generally, a humanized antibody comprises one ormore variable domains in which HVRs, e.g., CDRs, (or portions thereof)are derived from a non-human antibody, and FRs (or portions thereof) arederived from human antibody sequences. A humanized antibody optionallywill also comprise at least a portion of a human constant region. Insome embodiments, some FR residues in a humanized antibody aresubstituted with corresponding residues from a non-human antibody (e.g.,the antibody from which the HVR residues are derived), e.g., to restoreor improve antibody specificity or affinity.

Humanized antibodies and methods of making them are reviewed, e.g., inAlmagro and Fransson, Front. Biosci. 13:1619-1633 (2008), and arefurther described, e.g., in Riechmann et al., Nature 332:323-329 (1988);Queen et al., Proc. Nat'l Acad. Sci. USA 86:10029-10033 (1989); U.S.Pat. Nos. 5,821,337, 7,527,791, 6,982,321, and 7,087,409; Kashmiri etal., Methods 36:25-34 (2005) (describing SDR (a-CDR) grafting); Padlan,Mol. Immunol. 28:489498 (1991) (describing “resurfacing”); Dall'Acqua etal., Methods 36:43-60 (2005) (describing “FR shuffling”); and Osbourn etal., Methods 36:61-68 (2005) and Klimka et al., Br. J. Cancer,83:252-260 (2000) (describing the “guided selection” approach to FRshuffling).

Human framework regions that may be used for humanization include butare not limited to: framework regions selected using the “best-fit”method (see, e.g., Sims et al. J. Immunol. 151:2296 (1993)); frameworkregions derived from the consensus sequence of human antibodies of aparticular subgroup of light or heavy chain variable regions (see, e.g.,Carter et al. Proc. Natl. Acad. Sci. USA, 89:4285 (1992); and Presta etal. J. Immunol., 151:2623 (1993)); human mature (somatically mutated)framework regions or human germline framework regions (see, e.g.,Almagro and Fransson, Front. Biosci. 13:1619-1633 (2008)); and frameworkregions derived from screening FR libraries (see, e.g., Baca et al., J.Biol. Chem. 272:10678-10684 (1997) and Rosok et al., J. Biol. Chem.271:22611-22618 (1996)).

4. Human Antibodies

In certain embodiments, an antibody provided herein is a human antibody.Human antibodies can be produced using various techniques known in theart. Human antibodies are described generally in van Dijk and van deWinkel, Curr. Opin. Pharmacol. 5: 368-74 (2001) and Lonberg, Curr. Opin.Immunol. 20:450-459 (2008).

Human antibodies may be prepared by administering an immunogen to atransgenic animal that has been modified to produce intact humanantibodies or intact antibodies with human variable regions in responseto antigenic challenge. Such animals typically contain all or a portionof the human immunoglobulin loci, which replace the endogenousimmunoglobulin loci, or which are present extrachromosomally orintegrated randomly into the animal's chromosomes. In such transgenicmice, the endogenous immunoglobulin loci have generally beeninactivated. For review of methods for obtaining human antibodies fromtransgenic animals, see Lonberg, Nat. Biotech. 23:1117-1125 (2005). Seealso, e.g., U.S. Pat. Nos. 6,075,181 and 6,150,584 describing XENOMOUSE™technology; U.S. Pat. No. 5,770,429 describing HUMAB® technology; U.S.Pat. No. 7,041,870 describing K-M MOUSE® technology, and U.S. PatentApplication Publication No. US 2007/0061900, describing VELOCIMOUSE®technology). Human variable regions from intact antibodies generated bysuch animals may be further modified, e.g., by combining with adifferent human constant region.

Human antibodies can also be made by hybridoma-based methods. Humanmyeloma and mouse-human heteromyeloma cell lines for the production ofhuman monoclonal antibodies have been described. (See, e.g., Kozbor J.Immunol., 133: 3001 (1984); Brodeur et al., Monoclonal AntibodyProduction Techniques and Applications, pp. 51-63 (Marcel Dekker, Inc.,New York, 1987); and Boerner et al., J. Immunol., 147: 86 (1991).) Humanantibodies generated via human B-cell hybridoma technology are alsodescribed in Li et al., Proc. Nat. Acad. Sci. USA, 103:3557-3562 (2006).Additional methods include those described, for example, in U.S. Pat.No. 7,189,826 (describing production of monoclonal human IgM antibodiesfrom hybridoma cell lines) and Ni, Xiandai Mianyixue, 26(4):265-268(2006) (describing human-human hybridomas). Human hybridoma technology(Trioma technology) is also described in Vollmers and Brandlein,Histology and Histopathology, 20(3):927-937 (2005) and Vollmers andBrandlein, Methods and Findings in Experimental and ClinicalPharmacology, 27(3):185-91 (2005).

Human antibodies may also be generated by isolating Fv clone variabledomain sequences selected from human-derived phage display libraries.Such variable domain sequences may then be combined with a desired humanconstant domain. Techniques for selecting human antibodies from antibodylibraries are described below.

5. Library-Derived Antibodies

Antibodies of the invention may be isolated by screening combinatoriallibraries for antibodies with the desired activity or activities. Forexample, a variety of methods are known in the art for generating phagedisplay libraries and screening such libraries for antibodies possessingthe desired binding characteristics. Such methods are reviewed, e.g., inHoogenboom et al. in Methods in Molecular Biology 178:1-37 (O'Brien etal., ed., Human Press, Totowa, NJ, 2001) and further described, e.g., inthe McCafferty et al., Nature 348:552-554; Clackson et al., Nature 352:624-628 (1991); Marks et al., J. Mol. Biol. 222: 581-597 (1992); Marksand Bradbury, in Methods in Molecular Biology 248:161-175 (Lo, ed.,Human Press, Totowa, NJ, 2003); Sidhu et al., J. Mol. Biol. 338(2):299-310 (2004); Lee et al., J. Mol. Biol. 340(5): 1073-1093 (2004);Fellouse, Proc. Natl. Acad. Sci. USA 101(34): 12467-12472 (2004); andLee et al., J. Immunol. Methods 284(1-2): 119-132(2004).

In certain phage display methods, repertoires of VH and VL genes areseparately cloned by polymerase chain reaction (PCR) and recombinedrandomly in phage libraries, which can then be screened forantigen-binding phage as described in Winter et al., Ann. Rev. Immunol.,12: 433-455 (1994). Phage typically display antibody fragments, eitheras single-chain Fv (scFv) fragments or as Fab fragments. Libraries fromimmunized sources provide high-affinity antibodies to the immunogenwithout the requirement of constructing hybridomas. Alternatively, thenaïve repertoire can be cloned (e.g., from human) to provide a singlesource of antibodies to a wide range of non-self and also self antigenswithout any immunization as described by Griffiths et al., EMBO J, 12:725-734 (1993). Finally, naïve libraries can also be made syntheticallyby cloning unrearranged V-gene segments from stem cells, and using PCRprimers containing random sequence to encode the highly variable CDR3regions and to accomplish rearrangement in vitro, as described byHoogenboom and Winter, J. Mol. Biol., 227: 381-388 (1992). Patentpublications describing human antibody phage libraries include, forexample: U.S. Pat. No. 5,750,373, and US Patent Publication Nos.2005/0079574, 2005/0119455, 2005/0266000, 2007/0117126, 2007/0160598,2007/0237764, 2007/0292936, and 2009/0002360.

Antibodies or antibody fragments isolated from human antibody librariesare considered human antibodies or human antibody fragments herein.

6. Multispecific Antibodies

In certain embodiments, an antibody provided herein is a multispecificantibody, e.g. a bispecific antibody. Multispecific antibodies aremonoclonal antibodies that have binding specificities for at least twodifferent sites. In certain embodiments, one of the bindingspecificities is for a first antigen and the other is for any otherantigen. In certain embodiments, bispecific antibodies may bind to twodifferent epitopes of the first antigen. Bispecific antibodies may alsobe used to localize cytotoxic agents to cells which express the firstantigen. Bispecific antibodies can be prepared as full length antibodiesor antibody fragments.

Techniques for making multispecific antibodies include, but are notlimited to, recombinant co-expression of two immunoglobulin heavychain-light chain pairs having different specificities (see Milstein andCuello, Nature 305: 537 (1983)), WO 93/08829, and Traunecker et al.,EMBO J. 10: 3655 (1991)), and “knob-in-hole” engineering (see, e.g.,U.S. Pat. No. 5,731,168). Multi-specific antibodies may also be made byengineering electrostatic steering effects for making antibodyFc-heterodimeric molecules (WO 2009/089004A1); cross-linking two or moreantibodies or fragments (see, e.g., U.S. Pat. No. 4,676,980, and Brennanet al., Science, 229: 81 (1985)); using leucine zippers to producebi-specific antibodies (see, e.g., Kostelny et al., J. Immunol.,148(5):1547-1553 (1992)); using “diabody” technology for makingbispecific antibody fragments (see, e.g., Hollinger et al., Proc. Natl.Acad. Sci. USA, 90:6444-6448 (1993)); and using single-chain Fv (sFv)dimers (see, e.g. Gruber et al., J. Immunol., 152:5368 (1994)); andpreparing trispecific antibodies as described, e.g., in Tutt et al. J.Immunol. 147: 60 (1991).

Engineered antibodies with three or more functional antigen bindingsites, including “Octopus antibodies,” are also included herein (see,e.g. US 2006/0025576A1).

The antibody or fragment herein also includes a “Dual Acting FAb” or“DAF” comprising an antigen binding site that binds to a first antigenas well as another, different antigen (see, US 2008/0069820, forexample).

7. Antibody Variants

In certain embodiments, amino acid sequence variants of the antibodiesprovided herein are contemplated. For example, it may be desirable toimprove the binding affinity and/or other biological properties of theantibody. Amino acid sequence variants of an antibody may be prepared byintroducing appropriate modifications into the nucleotide sequenceencoding the antibody, or by peptide synthesis. Such modificationsinclude, for example, deletions from, and/or insertions into and/orsubstitutions of residues within the amino acid sequences of theantibody. Any combination of deletion, insertion, and substitution canbe made to arrive at the final construct, provided that the finalconstruct possesses the desired characteristics, e.g., antigen-binding.

a) Substitution, Insertion, and Deletion Variants

In certain embodiments, antibody variants having one or more amino acidsubstitutions are provided. Sites of interest for substitutionalmutagenesis include the HVRs and FRs. Conservative substitutions areshown in Table 1 under the heading of “conservative substitutions.” Moresubstantial changes are provided in Table 1 under the heading of“exemplary substitutions,” and as further described below in referenceto amino acid side chain classes. Amino acid substitutions may beintroduced into an antibody of interest and the products screened for adesired activity, e.g., retained/improved antigen binding, decreasedimmunogenicity, or improved ADCC or CDC.

TABLE 1 Preferred Original Exemplary Substi- Residue Substitutionstutions Ala (A) Val; Leu; Ile Val Arg (R) Lys; Gln; Asn Lys Asn (N) Gln;His; Asp, Lys; Arg Gln Asp (D) Glu; Asn Glu Cys (C) Ser; Ala Ser Gln (Q)Asn; Glu Asn Glu (E) Asp; Gln Asp Gly (G) Ala Ala His (H) Asn; Gln; Lys;Arg Arg Ile (I) Leu; Val; Met; Ala; Phe; Norleucine Leu Leu (L)Norleucine; Ile; Val; Met; Ala; Phe Ile Lys (K) Arg; Gln; Asn Arg Met(M) Leu; Phe; Ile Leu Phe (F) Trp; Leu; Val; Ile; Ala; Tyr Tyr Pro (P)Ala Ala Ser (S) Thr Thr Thr (T) Val; Ser Ser Trp (W) Tyr; Phe Tyr Tyr(Y) Trp; Phe; Thr; Ser Phe Val (V) Ile; Leu; Met; Phe; Ala; NorleucineLeu

Amino acids may be grouped according to common side-chain properties:

-   -   (1) hydrophobic: Norleucine, Met, Ala, Val, Leu, Ile;    -   (2) neutral hydrophilic: Cys, Ser, Thr, Asn, Gln;    -   (3) acidic: Asp, Glu;    -   (4) basic: His, Lys, Arg;    -   (5) residues that influence chain orientation: Gly, Pro;    -   (6) aromatic: Trp, Tyr, Phe.

Non-conservative substitutions will entail exchanging a member of one ofthese classes for another class.

One type of substitutional variant involves substituting one or morehypervariable region residues of a parent antibody (e.g. a humanized orhuman antibody). Generally, the resulting variant(s) selected forfurther study will have modifications (e.g., improvements) in certainbiological properties (e.g., increased affinity, reduced immunogenicity)relative to the parent antibody and/or will have substantially retainedcertain biological properties of the parent antibody. An exemplarysubstitutional variant is an affinity matured antibody, which may beconveniently generated, e.g., using phage display-based affinitymaturation techniques such as those described herein. Briefly, one ormore HVR residues are mutated and the variant antibodies displayed onphage and screened for a particular biological activity (e.g. bindingaffinity).

Alterations (e.g., substitutions) may be made in HVRs, e.g., to improveantibody affinity. Such alterations may be made in HVR “hotspots,” i.e.,residues encoded by codons that undergo mutation at high frequencyduring the somatic maturation process (see, e.g., Chowdhury, MethodsMol. Biol. 207:179-196 (2008)), and/or SDRs (a-CDRs), with the resultingvariant VH or VL being tested for binding affinity. Affinity maturationby constructing and reselecting from secondary libraries has beendescribed, e.g., in Hoogenboom et al. in Methods in Molecular Biology178:1-37 (O'Brien et al., ed., Human Press, Totowa, NJ, (2001).) In someembodiments of affinity maturation, diversity is introduced into thevariable genes chosen for maturation by any of a variety of methods(e.g., error-prone PCR, chain shuffling, or oligonucleotide-directedmutagenesis). A secondary library is then created. The library is thenscreened to identify any antibody variants with the desired affinity.Another method to introduce diversity involves HVR-directed approaches,in which several HVR residues (e.g., 4-6 residues at a time) arerandomized. HVR residues involved in antigen binding may be specificallyidentified, e.g., using alanine scanning mutagenesis or modeling. CDR-H3and CDR-L3 in particular are often targeted.

In certain embodiments, substitutions, insertions, or deletions mayoccur within one or more HVRs so long as such alterations do notsubstantially reduce the ability of the antibody to bind antigen. Forexample, conservative alterations (e.g., conservative substitutions asprovided herein) that do not substantially reduce binding affinity maybe made in HVRs. Such alterations may be outside of HVR “hotspots” orSDRs. In certain embodiments of the variant VH and VL sequences providedabove, each HVR either is unaltered, or contains no more than one, twoor three amino acid substitutions.

A useful method for identification of residues or regions of an antibodythat may be targeted for mutagenesis is called “alanine scanningmutagenesis” as described by Cunningham and Wells (1989) Science,244:1081-1085. In this method, a residue or group of target residues(e.g., charged residues such as arg, asp, his, lys, and glu) areidentified and replaced by a neutral or negatively charged amino acid(e.g., alanine or polyalanine) to determine whether the interaction ofthe antibody with antigen is affected. Further substitutions may beintroduced at the amino acid locations demonstrating functionalsensitivity to the initial substitutions. Alternatively, oradditionally, a crystal structure of an antigen-antibody complex toidentify contact points between the antibody and antigen. Such contactresidues and neighboring residues may be targeted or eliminated ascandidates for substitution. Variants may be screened to determinewhether they contain the desired properties.

Amino acid sequence insertions include amino- and/or carboxyl-terminalfusions ranging in length from one residue to polypeptides containing ahundred or more residues, as well as intrasequence insertions of singleor multiple amino acid residues. Examples of terminal insertions includean antibody with an N-terminal methionyl residue. Other insertionalvariants of the antibody molecule include the fusion to the N- orC-terminus of the antibody to an enzyme (e.g. for ADEPT) or apolypeptide which increases the serum half-life of the antibody.

b) Glycosylation Variants

In certain embodiments, an antibody provided herein is altered toincrease or decrease the extent to which the antibody is glycosylated.Addition or deletion of glycosylation sites to an antibody may beconveniently accomplished by altering the amino acid sequence such thatone or more glycosylation sites is created or removed.

Where the antibody comprises an Fc region, the carbohydrate attachedthereto may be altered. Native antibodies produced by mammalian cellstypically comprise a branched, biantennary oligosaccharide that isgenerally attached by an N-linkage to Asn297 of the CH2 domain of the Fcregion. See, e.g., Wright et al. TIBTECH 15:26-32 (1997). Theoligosaccharide may include various carbohydrates, e.g., mannose,N-acetyl glucosamine (GlcNAc), galactose, and sialic acid, as well as afucose attached to a GlcNAc in the “stem” of the biantennaryoligosaccharide structure. In some embodiments, modifications of theoligosaccharide in an antibody of the invention may be made in order tocreate antibody variants with certain improved properties.

In one embodiment, antibody variants are provided having a carbohydratestructure that lacks fucose attached (directly or indirectly) to an Fcregion. For example, the amount of fucose in such antibody may be from1% to 80%, from 1% to 65%, from 5% to 65% or from 20% to 40%. The amountof fucose is determined by calculating the average amount of fucosewithin the sugar chain at Asn297, relative to the sum of allglycostructures attached to Asn 297 (e. g. complex, hybrid and highmannose structures) as measured by MALDI-TOF mass spectrometry, asdescribed in WO 2008/077546, for example. Asn297 refers to theasparagine residue located at about position 297 in the Fc region (Eunumbering of Fc region residues); however, Asn297 may also be locatedabout ±3 amino acids upstream or downstream of position 297, i.e.,between positions 294 and 300, due to minor sequence variations inantibodies. Such fucosylation variants may have improved ADCC function.See, e.g., US Patent Publication Nos. US 2003/0157108 (Presta, L.); US2004/0093621 (Kyowa Hakko Kogyo Co., Ltd). Examples of publicationsrelated to “defucosylated” or “fucose-deficient” antibody variantsinclude: US 2003/0157108; WO 2000/61739; WO 2001/29246; US 2003/0115614;US 2002/0164328; US 2004/0093621; US 2004/0132140; US 2004/0110704; US2004/0110282; US 2004/0109865; WO 2003/085119; WO 2003/084570; WO2005/035586; WO 2005/035778; WO2005/053742; WO2002/031140; Okazaki etal. J. Mol. Biol. 336:1239-1249 (2004); Yamane-Ohnuki et al. Biotech.Bioeng. 87: 614 (2004). Examples of cell lines capable of producingdefucosylated antibodies include Lec13 CHO cells deficient in proteinfucosylation (Ripka et al. Arch. Biochem. Biophys. 249:533-545 (1986);US Pat Appl No US 2003/0157108 A1, Presta, L; and WO 2004/056312 A1,Adams et al., especially at Example 11), and knockout cell lines, suchas alpha-1,6-fucosyltransferase gene, FUT8, knockout CHO cells (see,e.g., Yamane-Ohnuki et al. Biotech. Bioeng. 87: 614 (2004); Kanda, Y. etal., Biotechnol. Bioeng., 94(4):680-688 (2006); and WO2003/085107).

Antibodies variants are further provided with bisected oligosaccharides,e.g., in which a biantennary oligosaccharide attached to the Fc regionof the antibody is bisected by GlcNAc. Such antibody variants may havereduced fucosylation and/or improved ADCC function. Examples of suchantibody variants are described, e.g., in WO 2003/011878 (Jean-Mairet etal.); U.S. Pat. No. 6,602,684 (Umana et al.); and US 2005/0123546 (Umanaet al.). Antibody variants with at least one galactose residue in theoligosaccharide attached to the Fc region are also provided. Suchantibody variants may have improved CDC function. Such antibody variantsare described, e.g., in WO 1997/30087 (Patel et al.); WO 1998/58964(Raju, S.); and WO 1999/22764 (Raju, S.).

c) Fe Region Variants

In certain embodiments, one or more amino acid modifications may beintroduced into the Fc region of an antibody provided herein, therebygenerating an Fc region variant. The Fc region variant may comprise ahuman Fc region sequence (e.g., a human IgG1, IgG2, IgG3 or IgG4 Fcregion) comprising an amino acid modification (e.g. a substitution) atone or more amino acid positions.

In certain embodiments, the invention contemplates an antibody variantthat possesses some but not all effector functions, which make it adesirable candidate for applications in which the half life of theantibody in vivo is important yet certain effector functions (such ascomplement and ADCC) are unnecessary or deleterious. In vitro and/or invivo cytotoxicity assays can be conducted to confirm thereduction/depletion of CDC and/or ADCC activities. For example, Fcreceptor (FcR) binding assays can be conducted to ensure that theantibody lacks FcγR binding (hence likely lacking ADCC activity), butretains FcRn binding ability. The primary cells for mediating ADCC, NKcells, express Fc(RIII only, whereas monocytes express Fc(RI, Fc(RII andFc(RIII FcR expression on hematopoietic cells is summarized in Table 3on page 464 of Ravetch and Kinet, Annu. Rev. Immunol. 9:457-492 (1991).Non-limiting examples of in vitro assays to assess ADCC activity of amolecule of interest is described in U.S. Pat. No. 5,500,362 (see, e.g.Hellstrom, I. et al. Proc. Nat'l Acad. Sci. USA 83:7059-7063 (1986)) andHellstrom, I et al., Proc. Nat'l Acad. Sci. USA 82:1499-1502 (1985);5,821,337 (see Bruggemann, M. et al., J. Exp. Med. 166:1351-1361(1987)). Alternatively, non-radioactive assays methods may be employed(see, for example, ACTI™ non-radioactive cytotoxicity assay for flowcytometry (CellTechnology, Inc. Mountain View, CA; and CytoTox 96® nonradioactive cytotoxicity assay (Promega, Madison, WI). Useful effectorcells for such assays include peripheral blood mononuclear cells (PBMC)and Natural Killer (NK) cells. Alternatively, or additionally, ADCCactivity of the molecule of interest may be assessed in vivo, e.g., in aanimal model such as that disclosed in Clynes et al. Proc. Nat'l Acad.Sci. USA 95:652-656 (1998). C1q binding assays may also be carried outto confirm that the antibody is unable to bind C1q and hence lacks CDCactivity. See, e.g., C1q and C3c binding ELISA in WO 2006/029879 and WO2005/100402. To assess complement activation, a CDC assay may beperformed (see, for example, Gazzano-Santoro et al., J. Immunol. Methods202:163 (1996); Cragg, M. S. et al., Blood 101:1045-1052 (2003); andCragg, M. S. and M. J. Glennie, Blood 103:2738-2743 (2004)). FcRnbinding and in vivo clearance/half life determinations can also beperformed using methods known in the art (see, e.g., Petkova, S. B. etal., Int'l. Immunol. 18(12):1759-1769 (2006)).

Antibodies with reduced effector function include those withsubstitution of one or more of Fc region residues 238, 265, 269, 270,297, 327 and 329 (U.S. Pat. No. 6,737,056). Such Fc mutants include Fcmutants with substitutions at two or more of amino acid positions 265,269, 270, 297 and 327, including the so-called “DANA” Fc mutant withsubstitution of residues 265 and 297 to alanine (U.S. Pat. No.7,332,581).

Certain antibody variants with improved or diminished binding to FcRsare described. (See, e.g., U.S. Pat. No. 6,737,056; WO 2004/056312, andShields et al., J. Biol. Chem. 9(2): 6591-6604 (2001).)

In certain embodiments, an antibody variant comprises an Fc region withone or more amino acid substitutions which improve ADCC, e.g.,substitutions at positions 298, 333, and/or 334 of the Fc region (EUnumbering of residues).

In some embodiments, alterations are made in the Fc region that resultin altered (i.e., either improved or diminished) C1q binding and/orComplement Dependent Cytotoxicity (CDC), e.g., as described in U.S. Pat.No. 6,194,551, WO 99/51642, and Idusogie et al. J. Immunol. 164:4178-4184 (2000).

Antibodies with increased half lives and improved binding to theneonatal Fc receptor (FcRn), which is responsible for the transfer ofmaternal IgGs to the fetus (Guyer et al., J. Immunol. 117:587 (1976) andKim et al., J. Immunol. 24:249 (1994)), are described inUS2005/0014934A1 (Hinton et al.). Those antibodies comprise an Fc regionwith one or more substitutions therein which improve binding of the Fcregion to FcRn. Such Fc variants include those with substitutions at oneor more of Fc region residues: 238, 256, 265, 272, 286, 303, 305, 307,311, 312, 317, 340, 356, 360, 362, 376, 378, 380, 382, 413, 424 or 434,e.g., substitution of Fc region residue 434 (U.S. Pat. No. 7,371,826).

See also Duncan & Winter, Nature 322:738-40 (1988); U.S. Pat. Nos.5,648,260; 5,624,821; and WO 94/29351 concerning other examples of Fcregion variants.

d) Cysteine Engineered Antibody Variants

In certain embodiments, it may be desirable to create cysteineengineered antibodies, e.g., “thioMAbs,” in which one or more residuesof an antibody are substituted with cysteine residues. In particularembodiments, the substituted residues occur at accessible sites of theantibody. By substituting those residues with cysteine, reactive thiolgroups are thereby positioned at accessible sites of the antibody andmay be used to conjugate the antibody to other moieties, such as drugmoieties or linker-drug moieties, to create an immunoconjugate, asdescribed further herein. In certain embodiments, any one or more of thefollowing residues may be substituted with cysteine: V205 (Kabatnumbering) of the light chain; A118 (EU numbering) of the heavy chain;and S400 (EU numbering) of the heavy chain Fc region. Cysteineengineered antibodies may be generated as described, e.g., in U.S. Pat.No. 7,521,541.

e) Antibody Derivatives

In certain embodiments, an antibody provided herein may be furthermodified to contain additional nonproteinaceous moieties that are knownin the art and readily available. The moieties suitable forderivatization of the antibody include but are not limited to watersoluble polymers. Non-limiting examples of water soluble polymersinclude, but are not limited to, polyethylene glycol (PEG), copolymersof ethylene glycol/propylene glycol, carboxymethylcellulose, dextran,polyvinyl alcohol, polyvinyl pyrrolidone, poly-1,3-dioxolane,poly-1,3,6-trioxane, ethylene/maleic anhydride copolymer, polyaminoacids(either homopolymers or random copolymers), and dextran or poly(n-vinylpyrrolidone)polyethylene glycol, propropylene glycol homopolymers,prolypropylene oxide/ethylene oxide co-polymers, polyoxyethylatedpolyols (e.g., glycerol), polyvinyl alcohol, and mixtures thereof.Polyethylene glycol propionaldehyde may have advantages in manufacturingdue to its stability in water. The polymer may be of any molecularweight, and may be branched or unbranched. The number of polymersattached to the antibody may vary, and if more than one polymer areattached, they can be the same or different molecules. In general, thenumber and/or type of polymers used for derivatization can be determinedbased on considerations including, but not limited to, the particularproperties or functions of the antibody to be improved, whether theantibody derivative will be used in a therapy under defined conditions,etc.

In another embodiment, conjugates of an antibody and nonproteinaceousmoiety that may be selectively heated by exposure to radiation areprovided. In one embodiment, the nonproteinaceous moiety is a carbonnanotube (Kam et al., Proc. Natl. Acad. Sci. USA 102: 11600-11605(2005)). The radiation may be of any wavelength, and includes, but isnot limited to, wavelengths that do not harm ordinary cells, but whichheat the nonproteinaceous moiety to a temperature at which cellsproximal to the antibody-nonproteinaceous moiety are killed.

Recombinant Methods and Compositions

Antibodies may be produced using recombinant methods and compositions,e.g., as described in U.S. Pat. No. 4,816,567. In one embodiment,isolated nucleic acid encoding an antibody described herein is provided.Such nucleic acid may encode an amino acid sequence comprising the VLand/or an amino acid sequence comprising the VH of the antibody (e.g.,the light and/or heavy chains of the antibody). In a further embodiment,one or more vectors (e.g., expression vectors) comprising such nucleicacid are provided. In a further embodiment, a host cell comprising suchnucleic acid is provided. In one such embodiment, a host cell comprises(e.g., has been transformed with): (1) a vector comprising a nucleicacid that encodes an amino acid sequence comprising the VL of theantibody and an amino acid sequence comprising the VH of the antibody,or (2) a first vector comprising a nucleic acid that encodes an aminoacid sequence comprising the VL of the antibody and a second vectorcomprising a nucleic acid that encodes an amino acid sequence comprisingthe VH of the antibody. In one embodiment, the host cell is eukaryotic,e.g. a Chinese Hamster Ovary (CHO) cell or lymphoid cell (e.g., Y0, NS0,Sp20 cell). In one embodiment, a method of making an antibody isprovided, wherein the method comprises culturing a host cell comprisinga nucleic acid encoding the antibody, as provided above, underconditions suitable for expression of the antibody, and optionallyrecovering the antibody from the host cell (or host cell culturemedium).

For recombinant production of an antibody, nucleic acid encoding anantibody, e.g., as described above, is isolated and inserted into one ormore vectors for further cloning and/or expression in a host cell. Suchnucleic acid may be readily isolated and sequenced using conventionalprocedures (e.g., by using oligonucleotide probes that are capable ofbinding specifically to genes encoding the heavy and light chains of theantibody).

Suitable host cells for cloning or expression of antibody-encodingvectors include prokaryotic or eukaryotic cells described herein. Forexample, antibodies may be produced in bacteria, in particular whenglycosylation and Fc effector function are not needed. For expression ofantibody fragments and polypeptides in bacteria, see, e.g., U.S. Pat.Nos. 5,648,237, 5,789,199, and 5,840,523. (See also Charlton, Methods inMolecular Biology, Vol. 248 (B.K.C. Lo, ed., Humana Press, Totowa, N J,2003), pp. 245-254, describing expression of antibody fragments in E.coli.) After expression, the antibody may be isolated from the bacterialcell paste in a soluble fraction and can be further purified.

In addition to prokaryotes, eukaryotic microbes such as filamentousfungi or yeast are suitable cloning or expression hosts forantibody-encoding vectors, including fungi and yeast strains whoseglycosylation pathways have been “humanized,” resulting in theproduction of an antibody with a partially or fully human glycosylationpattern. See Gerngross, Nat. Biotech. 22:1409-1414 (2004), and Li etal., Nat. Biotech. 24:210-215 (2006).

Suitable host cells for the expression of glycosylated antibody are alsoderived from multicellular organisms (invertebrates and vertebrates).Examples of invertebrate cells include plant and insect cells. Numerousbaculoviral strains have been identified which may be used inconjunction with insect cells, particularly for transfection ofSpodoptera frugiperda cells.

Plant cell cultures can also be utilized as hosts. See, e.g., U.S. Pat.Nos. 5,959,177, 6,040,498, 6,420,548, 7,125,978, and 6,417,429(describing PLANTIBODIES™ technology for producing antibodies intransgenic plants).

Vertebrate cells may also be used as hosts. For example, mammalian celllines that are adapted to grow in suspension may be useful. Otherexamples of useful mammalian host cell lines are monkey kidney CV1 linetransformed by SV40 (COS-7); human embryonic kidney line (293 or 293cells as described, e.g., in Graham et al., J. Gen Virol. 36:59 (1977));baby hamster kidney cells (BHK); mouse sertoli cells (TM4 cells asdescribed, e.g., in Mather, Biol. Reprod. 23:243-251 (1980)); monkeykidney cells (CV1); African green monkey kidney cells (VERO-76); humancervical carcinoma cells (HELA); canine kidney cells (MDCK; buffalo ratliver cells (BRL 3A); human lung cells (W138); human liver cells (HepG2); mouse mammary tumor (MMT 060562); TRI cells, as described, e.g., inMather et al., Annals N.Y. Acad. Sci. 383:44-68 (1982); MRC 5 cells; andFS4 cells. Other useful mammalian host cell lines include Chinesehamster ovary (CHO) cells, including DHFR⁻ CHO cells (Urlaub et al.,Proc. Natl. Acad. Sci. USA 77:4216 (1980)); and myeloma cell lines suchas Y0, NS0 and Sp2/0. For a review of certain mammalian host cell linessuitable for antibody production, see, e.g., Yazaki and Wu, Methods inMolecular Biology, Vol. 248 (B.K.C. Lo, ed., Humana Press, Totowa, NJ),pp. 255-268 (2003).

Assays

Antibodies provided herein may be identified, screened for, orcharacterized for their physical/chemical properties and/or biologicalactivities by various assays known in the art.

I. Binding Assays and Other Assays

In one aspect, an antibody of the invention is tested for its antigenbinding activity, e.g., by known methods such as ELISA, Western blot,etc.

In another aspect, competition assays may be used to identify anantibody that competes with an antibody of the invention for binding toan antigen of interest. In certain embodiments, such a competingantibody binds to the same epitope (e.g., a linear or a conformationalepitope) that is bound by an antibody of the invention. Detailedexemplary methods for mapping an epitope to which an antibody binds areprovided in Morris (1996) “Epitope Mapping Protocols,” in Methods inMolecular Biology vol. 66 (Humana Press, Totowa, NJ).

In an exemplary competition assay, immobilized antigen of interest isincubated in a solution comprising a first labeled antibody that bindsto antigen of interest (e.g., an antibody of the invention) and a secondunlabeled antibody that is being tested for its ability to compete withthe first antibody for binding to antigen of interest. The secondantibody may be present in a hybridoma supernatant. As a control,immobilized antigen of interest is incubated in a solution comprisingthe first labeled antibody but not the second unlabeled antibody. Afterincubation under conditions permissive for binding of the first antibodyto antigen of interest, excess unbound antibody is removed, and theamount of label associated with immobilized antigen of interest ismeasured. If the amount of label associated with immobilized antigen ofinterest is substantially reduced in the test sample relative to thecontrol sample, then that indicates that the second antibody iscompeting with the first antibody for binding to antigen of interest.See Harlow and Lane (1988) Antibodies: A Laboratory Manual ch.14 (ColdSpring Harbor Laboratory, Cold Spring Harbor, NY).

2. Activity Assays

In one aspect, assays are provided for identifying antibodies thereofhaving biological activity. Antibodies having such biological activityin vivo and/or in vitro are also provided.

In certain embodiments, an antibody of the invention is tested for suchbiological activity.

The following examples are offered for illustrative purposes only, andare not intended to limit the scope of the present invention in any way.

All patent and literature references cited in the present specificationare hereby expressly incorporated by reference in their entirety.

III. Examples

The following are examples of methods and compositions of the invention.It is understood that various other embodiments may be practiced, giventhe general description provided above.

M13KO7 helper phage were from New England Biolabs. Bovine serum albumin(BSA) and Tween 20 were from Sigma. Casein was from Pierce. anti-M13conjugated horse-radish peroxidase (HRP) was from Amersham Pharmacia.Maxisorp immunoplates were from NUNC. Tetramethylbenzidine (TMB)substrate was from Kirkegaard and Perry Laboratories. All other proteinantigens were generated by research groups at Genentech, Inc.

Example 1: Selection of Signal Sequence for Expression in Prokaryoticand Eukaryotic Cells

To address whether a vector is capable of expressing proteins ofinterest in both Escherichia coli and eukaryotic (mammalian) cells, foursignal sequences of non-bacterial origin for which there was anecdotalevidence supporting the idea that they could function in mammalian cellswere selected. We tested these signal sequences for their ability todrive display of an anti-Her2 (h4D5) Fab on M13 phage using a phageELISA (FIG. 1A). The levels of display were evaluated relative to thebacterial heat-stable enterotoxin II (STII) signal sequence. Thecapacity of the signal sequences to drive Fab-phage display variedgreatly, and one signal sequence, from the murine binding immunoglobulinprotein (mBiP), drove levels of display that could possibly allowefficient levels of Fab display.

To improve the performance of the mBiP signal sequence further, weutilized a phage-based codon optimization approach, as it has beendemonstrated previously that the function of eukaryotic signal sequencesin bacteria is greatly affected by codon usage (Humphreys et al., TheProtein Expression and Purification, 20: 252-264 (2000). A phage librarywas constructed in which the mBiP signal sequence was fused to theN-terminus of the h4D5 Fab HC in a standard phagemid vector. The DNAsequence of the mBiP signal peptide was diversified in the third base ofeach codon following the first two methionines allowing only silentmutations. After four rounds of solid-phase panning against immobilizedHer2, individual clones were picked and sequenced. We found that theconsensus sequence of the selected clones strongly favored an adenine orthymine in the randomized positions rather than a guanine or cytosine.This result is punctuated by the fact that 15 of the 17 codons in thewild-type mBiP sequence contain a guanine or cytosine in the third baseposition, but each of the 17 codons in the sorted library containedadenine or thymine in these positions 60-90% of the time. When tested ina phage ELISA, the optimized mBiP signal sequence drives display of h4D5Fab at levels comparable to the prokaryotic STII signal sequence,suggesting that the mBiP signal sequence can be utilized for phagedisplay and panning experiments in place of the prokaryotic STII signalsequence without any apparent reduction in performance (FIG. 1B).

Next, the ability of the mBiP signal sequence to support expression andsecretion of IgG in mammalian cells was evaluated. Mammalian expressionvectors encoding the HC and LC of h4D5 hIgG₁, each with the mBiP signalsequence fused to the N-terminus, were cotransfected into suspension293S cells and grown for five days, after which the supernatants werecollected and IgG was purified by affinity chromatography. The IgG yieldfrom one 30 mL culture was routinely ˜2.0 mg, comparable to the yieldsobtained using a native HC signal (VHS) in both chains (data not shown).Interestingly, use of the wild-type versus the codon optimized form ofthe mBiP signal sequence had no discernable effect on IgG expressionlevels (data not shown). Gel filtration chromatography and massspectrometry confirmed that the purified protein was >90% monomeric insolution and that the mBiP signal sequence was fully cleaved at theproper position on both HC and LC (data not shown). Because h4D5 isknown to be a good expresser, we tested the performance of mBiP relativeto VHS on a pool of uncharacterized clones arbitrarily selected from aphage panning experiment. The mean yield from these clones was ˜1.0 mgfrom a 30 mL suspension culture, and no significant differences wereobserved between the two signal sequences (FIGS. 2A and B).

In summary, the mBiP mammalian secretion signal sequence was capable ofexpressing IgG in mammalian cells at levels sufficient for screening,and once codon optimized, was also capable of driving robust Fab displayon phage without compromising IgG expression levels.

Example 2: Expression of Alternate Fab Fusions in Prokaryotic andEukaryotic Cells

In order to generate different Fab-fusion proteins in a hostcell-dependent manner, we sought to exploit the natural process ofintron splicing which occurs during mRNA processing in eukaryotic, butnot prokaryotic cells. The genomic sequence of hIgG₁ HC constant regioncontains three natural introns (FIG. 3A). The first of these (Intron1)is a 384 base pair intron positioned between the HC variable domain(V_(H)) and the hinge region. A HC expression vector containing Intron1and an optimized splice donor sequence expressed fully spliced mRNA asassessed by RT-PCR and sequencing of the transcripts and, whencotransfected with a LC vector, expressed IgG₁ at levels comparable to avector without the intron (FIG. 5 ).

To determine whether the Fab fragment to a phage adaptor peptideembedded within the Intron1 sequence allows both display on phage andIgG expression in bacterial and mammalian cells, respectively, anadaptor peptide (FIG. 3B) or the phage coat protein gene-III (FIG. 3C)was inserted into the h4D5 HC.Intron1 construct at the 5′ end of Intron1 or Intron 3. The natural splice donor from Intron 1 or 3 was movedimmediately upstream of the adaptor peptide. When the HC-adaptor.Intron1construct was co-expressed with h4D5 LC in mammalian cells, theexpression of h4D5 IgG was approximately 40% (for the adaptor-containingintron) or 5% (for the gene-III-containing intron) that of the controlconstruct with no intron (FIG. 4A). RT-PCR demonstrated that, while afraction of the HC-adaptor mRNA was properly spliced (FIG. 4B, middleband), a significant amount of the mRNA was either unspliced (FIG. 4B,upper band) or incorrectly spliced from a cryptic splice donor in theV_(H) region (FIG. 4B, lower band). HC-gene-III mRNA was almostcompletely spliced from the cryptic splice donor. Silent mutation of thecryptic splice donor sequence resulted in accumulation of un-splicedmRNA only (not shown).

In light of the failure of the intron to efficiently splice when theadaptor sequence was inserted, we compared the sequence of the naturalsplice donor to the known consensus sequence of splice donors formammalian mRNAs (Stephens et al., J of Molecular Biology, 228: 1124-1136(1992)). As shown in FIG. 5 , the natural splice donor from hIgG₁Intron1 differs from the consensus donor sequence at three out of eightpositions. Substitutions at positions 1 and 5 were analyzed further, asthese positions are more conserved than position 8. A mutant splicedonor (Donor1) in which the bases at positions 1 and 5 were changed tomatch the consensus sequence (FIG. 5A) was generated and tested theability of these modified donors to mediate splicing of the syntheticintron in HC. This optimized splice donor completely restored splicingof the synthetic intron (FIG. 5B) with a concomitant increase in h4D5IgG expression to a level that matched that of the control constructcontaining no intron (FIG. 5C). The improvement in splicing and IgGexpression was observed whether the synthetic intron contains theadaptor peptide or gene-III and also whether the synthetic intron isbased on the hIgG1 intron 1 or intron 3.

Example 3: Generation of Expression and Secretion System for Prokaryoticand Eukaryotic Cells

For generation of the dual vector plasmid, we used the pBR322-derivedphagemid vector currently used for phage display, pRS. This bi-cistronicvector consists of a bacterial PhoA promoter driving expression of anantibody light chain cassette with its associated STII signal sequence,followed antibody heavy chain cassette with its associated STII signalsequence. At the end of the light chain sequence, there is a gD epitopetag for detection of Fab display on phage particles. In conventionalphagemids, the heavy chain sequence consists only of the V_(H) andC_(H)1 domains of hIgG and is fused at the nucleotide level to a utilitypeptide, such as a phage fusion protein, most often gene-III, whichencodes the phage coat protein pIII or an adaptor peptide. The 3′ end ofthe light chain and heavy chain cassettes contain a lambdatranscriptional terminator sequence for halting transcription in E.coli. Because this vector produces light chain and heavy chain-pIII froma single mRNA transcript, there are no transcriptional regulatoryelements between the LC and HC sequences. The vector also contains thebeta-lactamase (bla) gene to confer ampicillin resistance, the pMB1origin for replication in E. coli, and f1 origin for expression ofpillus on the bacterial surface, allowing for infection by M13 phage.Another form of this vector also includes the SV40 origin of replicationfor episomal replication of the plasmid in appropriate strains ofmammalian cells.

For construction of the initial dual vector (referred to herein as“pDV.6.0”), we first inserted the mammalian CMV promoter from pRK (amammalian expression vector used for expression of IgGs and otherproteins) upstream of the PhoA promoter driving the LC-HC cistron. Atthe end of the LC antibody coding sequence, we inserted an Amber stopcodon followed by a gD epitope tag, allowing detection of tagged LCs onphage when displayed in an Amber suppressor E. coli strain. The epitopetag is absent when the vector is expressed in mammalian cells. Thus, theLC cassette comprises (in order from 5′ to 3′) a eukaryotic promoter, abacterial promoter, a signal sequence, an antibody light chain (LC)coding sequence, and an epitope tag (gD).

Next, between the HC and LC cassettes we inserted a synthetic cassettecomprising of (in order from 5′ to 3′) an SV40 mammalianpolyadenylation/transcriptional stop signal, a lambda terminatorsequence for transcriptional termination in E. coli, a CMV promoter anda PhoA promoter.

Next, an SV40 mammalian polyadenylation/transcriptional stop signal anda lambda terminator sequence were inserted after the HC cassette. The HCcassette comprises a signal sequence and an antibody heavy chain (HC)coding sequence.

To allow for secretion of the fusion protein(s) of interest in bothprokaryotic and eukaryotic cells, we replaced the STII signal sequencespreceding the LC and HC with the eukaryotic murine bindingimmunoglobulin protein (mBiP) signal sequence. Screening of severalcandidate signal sequences lead us to discover that this signal sequencewas capable of functioning in applications requiring prokaryoticexpression (i.e., phage display) and/or eukaryotic expression (i.e.,expression of IgG in mammalian cells), and that mBiP performed as wellin both of these settings as did the respective signal sequences whichwere employed prior to this work.

To allow for expression of Fab-phage in E. coli and IgG in mammaliancells, we generated a synthetic intron in the HC cassette. We modified anatural intron from human IgG1 intron 1 or intron 3 to create asynthetic intron containing a fusion protein (gene-III) for display onphage particles. The genomic sequence of intron 1 (or intron 3) fromhuman IgG1 was inserted immediately after the gene-III sequenceseparated by a stop codon to produce Fab HC-p3 fusions in E. coli. Theplacement of the natural splice donor octanucleotide at the 5′ flankingregion of the synthetic intron required two amino acid mutations in thehinge region when expressed in E. coli (E212G and P213K, Kabatnumbering), and the mutations to create the optimized splice donorresult in both of these residues being mutated to lysine. Thesemutations do not affect levels of display on phage (not shown) and, asthe phage hinge region is removed during the splicing process, would beabsent in the full-length IgG expressed in mammalian cells.

Alternatively, for utilization of adaptor phage display, we generated avector similar to the pDV6.0 vector described above with a differentsynthetic intron (referred to herein as pDV5.0, shown in FIG. 7 ). Thegene-III sequence was replaced with one of two members of a leucinezipper pair (herein called an “adaptor”). In this synthetic intron, theadaptor peptide sequence is followed by a stop codon and the genomicsequence of intron 1 or 3. In this construct, we also inserted aseparate bacterial expression cassette consisting of gene-III fused tothe cognate member of the leucine zipper pair. This separate bacterialexpression cassette was introduced upstream of the LC CMV promoter andis controlled by a PhoA promoter, contains the STII signal sequence torestrict expression of the adaptor-gene-III to E. coli, and contains alambda terminator immediately downstream. When expressed in E. coli, theheavy and light chains assemble in the periplasm to form Fab, and theadaptor fused to the heavy chain stably binds to the cognate adaptor onthe pIII-adaptor protein. Packaging of this assembled Fab-adaptor-pIIIcomplex into phage particles will yield phage displaying the Fab ofinterest. In addition, we generated a custom mutant of the KO7 helperphage in which the partner adaptor is fused to the N-terminus ofgene-III (adaptor-KO7). Infection of E. coli harboring pDV.5.0 withadaptor-KO7 results in all copies of pIII present on the mature phagemidbeing fused to the adaptor. As a result, all copies of pIII areavailable to associate with Fab-adaptor, rather than only those copiesof pIII that originated from pDV5. In some cases, however, a lower levelof display may be desirable when rare high-affinity clones are sought(e.g., in affinity maturation applications). In this case, infection ofE. coli harboring pDV.5.0 with conventional KO7 helper phage will resultin a mixture of adaptor-pIII (from pDV.5.0) and wild-type pIII (from KO7helper phage) being displayed on the phage particles. In this scenario,since only a subset of the overall pIII pool can associate withadaptor-Fab, the resulting display levels will be lower than whenadaptor-KO7 is used. This ability to modulate display levels simply bychoosing the appropriate helper phage is a unique advantage of thecurrent invention.

We evaluated the ability of pDV5.0 to express different IgGs inmammalian cells. The HCs and LCs from four different human IgGs weresubcloned into pDV5.0 and expressed in 293 cells. Somewhat surprisingly,the overall yields from pDV were consistently ˜10-fold lower than from atwo-plasmid system. However, the yields are still on the order of˜0.1-0.4 mg per 30 mL culture (FIG. 6B). This amount of material is morethan adequate for routine screening assays, and can easily be scaled upto 0.1-1 L or more if larger amounts of material are required. The IgGswere shown to be >90% monomeric in solution by gel filtrationchromatography.

Example 4: Construction of Mutant Helper Phage, M13KO7 with AmberMutation in Gene-III (AMBER KO7)

To enhance display of proteins fused to pIII on M13 phage, we generateda mutant helper phage, Amber KO7, using site-directed mutagenesis. AmberKO7 has an amber codon introduced in the M13KO7 helper phage genome bysite-directed mutagenesis. The nucleotide sequence of the pIII(nucleotides 1579 to 2853 of mutant helper phage Amber KO7 is shown inFIG. 8 .

To generate Amber KO7, helper phage M13KO7 was used to infectEscherichia coli CJ236 strain (genotype dut⁻lung⁻) and progeny virionsharvested to purify ssDNA using an ssDNA purification kit (QIAGEN). Asynthetic oligonucleotide (sequence5′-GTGAATTATCACCGTCACCGACCTAGGCCATTTGGGAATTAGAGCCA-3′) (SEQ ID NO: 23)was used to mutate gene-III in M13KO7 by oligonucleotide-directed sitemutagenesis. Mutagenized DNA was used to transform E. coli XL1-Bluecells (Agilent Technologies) and seeded on a lawn of uninfected XL1-Bluecells on soft agar plates. Plaques were individually picked and cellsgrown in LB media containing 50 μg/ml kanamycin. Double-strandedreplicative form (RF) DNA was extracted with a DNA miniprep kit andsequenced to confirm the presence of the amber stop mutation.Homogeneity of population was confirmed by AvrII restrictionendonuclease digestion and agar gel electrophoresis of RF DNA. Allrecombinant DNA manipulation steps were performed as described(Sambrook, J. et al., A Laboratory Manual, Third Edition, Cold SpringHarbor Laboratory Press, Cold Spring Harbor, N Y, 2001). The level ofFab display on phage particles produced using Amber KO7 was measured byphage ELISA. Antigen (Her2) was immobilized on immunoplates and phagebearing and anti-Her2 Fab were produced in XL1-Blue cells using eitherwild-type KO7 (WT KO7) or a modified M13KO7 harboring an Amber mutationin pIII (Amber KO7) helper phage. Binding was detected by incubatingwith a mouse anti-M13-HRP conjugate followed by TMB substrate ODmeasurement at 450 nm. The use of Amber KO7 resulted in higher displaylevels from a low-display phagemid (closed triangles) compared to thelevels achieved by the same phagemid when WT KO7 was used for phageproduction (closed squares) (FIG. 9 ). The level of Fab display with thelow-display phagemid using Amber KO7 (closed trianges) was also similarto the level of Fab display observed when using a high-display phagemidwith WT KO7 (open diamonds) (FIG. 9 ).

Example 5: Generation of an Expression and Secretion System forProkaryotic and Eukaryotic Cells for Generation of NaîVe HC-OnlyLibraries and Use of the System for Phage Panning

In addition to the direct and indirect fusion vectors featuringprokaryotic and eukaryotic promoters on both HC and LC (pDV5.0 andpDV6.0) described in Example 3, we generated a modified direct fusiondual vector construct (pDV.6.5 shown in FIG. 14 ) in which the Fab LC isfused to the STII signal sequence and is driven only by a bacterial PhoApromoter whereas the Fab HC (containing the gene-III-synthetic intronand hIgG Fc sequences for expression of a full-length hIgG1 HC inmammalian cells) was driven by both a eukaryotic CMV promoter and aprokaryotic PhoA promoter. This construct was used to recapitulate asynthetic human Fab library previously described (Lee, et al., Journalof Molecular Biology, 340. 1073-1093 (2004)), in which diversity isintroduced into the HC only. Expression of full-length IgG from thisvector requires cotransfection of a mammalian expression vector whichencodes a LC.

Phage-displayed libraries were generated using oligonucleotide-directed(Kunkel) mutagenesis and “stop template” versions of pDV.6.5 in whichstop codons (TAA) were placed into all three heavy-chain CDRs. Thesestops were repaired during the mutagenesis reaction by a mixture ofoligonucleotides that annealed over the regions encoding CDRH1, H2 andH3 and replaced codons at the positions chosen for randomization withdegenerate codons. Mutagenesis reactions were electroporated intoXL1-Blue cells, and the cultures were grown using a temperature shiftprotocol (37° C. for 4 hours followed by 36 hours at 30° C.) in 2YTbroth supplemented with Amber.KO7 helper phage, 50 μg/ml carbenicillinand 25 μg/ml kanamycin. Phage were harvested from the culture medium byprecipitation with PEG/NaCl. Each electroporation reaction used ˜5 ofDNA and resulted in 1×10⁸-7×10⁸ transformants.

Panning of a naïve phage library generated in this vector was performedagainst the human vascular endothelial growth factor (VEGF). For phagelibrary sorting, protein antigens were immobilized on Maxisorpimmunoplates and libraries were subjected to four to five rounds ofbinding selections. Wells were blocked alternatively using BSA or caseinin alternating rounds. Random clones selected from rounds 3 through 5were assayed using a phage ELISA to compare binding to target antigen(VEGF) and an irrelevant protein (Her2) for checking non-specificbinding. Briefly, phage clones were grown overnight in 1.6 mL of 2YTbroth supplemented with Amber.KO7 helper phage (Example 4). Supernatantswere bound to immobilized antigen or irrelevant protein-coated platesfor 1 hour at room temperature. After washing, bound phage was detectedusing an HRP-conjugated anti-M13 antibody (20 minutes at roomtemperature) followed by detection with TMB substrate. We isolatedmultiple clones which were ELISA positive for VEGF, but not for anirrelevant control protein (Her2) (FIG. 10 —bar graph).

DNA from these clones that demonstrated specificity for VEGF was thenused to express full-length IgG by contransfection with a mammalianexpression vector encoding the common LC in 293 cells in small scalesuspension cultures for expression of full-length hIgG1. 1 mL cultureswere transfected using Expifectamine or JetPEI according to themanufacturer's instructions and incubated at 37 degrees C./8% CO₂ for5-7 days. Scaled-up transfections were performed in 30 mL 293 cells.

Culture supernatants were then used to screen the IgGs for VEGF bindingin an Fc capture assay on a BIAcore T100 instrument (FIG. 11 ). IgGsupernatants from 1 mL cultures were used to screen for antigen binding.An anti-human Fc capture antibody was immobilized onto a series S CMSsensor chip (˜10,000 RU). Supernatants were sequentially flowed overflow cells 2, 3 and 4 (5 μL/min for 4 minutes) to allow capture of IgGfrom the supernatant (50-150 RU), after which antigen (100-1000 nM) wasflowed over the immobilized IgGs (30 μL/min for 2 minutes) to measurethe binding response.

Sequencing of the positive binders show eight unique sequences (heavychain CDR sequences are shown in FIG. 12 ) with positive bindingproperties (FIG. 12 ). The sequencing data (FIG. 12 ) combined with thephage ELISA (FIG. 10 ) and BiaCore data (FIG. 11 ) was used to select apool of eight anti-VEGF clones for further analysis.

Expression for these eight clones was scaled up to 100 mL chinesehamster overlay (CHO) cell cultures (see FIG. 15 ) and purified materialwas used to evaluate the ability of the anti-VEGF clones to block thebinding of VEGF to one of its cognate receptors (VEGFR1) via areceptor-blocking ELISA. Biotinylated hVEGF165 (2 nM) was incubated with3-fold serially diluted anti-VEGF antibodies (200 nM top concentration)in PBS/0.5% BSA/0.05% Tween-20. After 1-2 hours of incubation at roomtemperature, the mixtures were transferred to the VEGFR1-immobilizedplate and incubated for 15 minutes. VEGFR-1 bound VEGF was then detectedby streptavidin-HRP for 30 minutes followed by development with TMBsubstrate and the IC50 value was measured.

We identified one clone (VEGF55) with an IC₅₀ comparable to that ofbevicizumab, a commercial anti-VEGF antibody (FIG. 13 ). In this way, wewere able to move directly from phage panning to IgG expression andtriage a pool of clones down to a single candidate, all without therequirement to subclone.

In summary, this modified direct fusion dual vector (pDV.6.5) was ableto be used for the construction of phage display libraries withrandomized heavy chains and constant light chains in E. coli and wasalso able to be used to subsequently express selected clones as nativeIgG1 in mammalian cells without subcloning when complemented with alight chain expression vector. Because the mammalian CMV promoter ispresent upstream of HC only, pDV expressed both Fab LC and Fab HC-pIIIin E. coli, but expressed only hIgG1HC in mammalian cells. This vectorwas used to select Fab fragments from a naïve synthetic Fab librarybinding multiple antigens, and then to express full-length native hIgG1from the selected clones in mammalian 293 and CHO cells bycotransfecting the modified direct fusion dual vector clones with amammalian expression vector encoding a common LC. Native IgG1 wasobtained from these expression experiments to conduct several assays,such that from a pool of 8 unique anti-VEGF clones showing bindingactivity by ELISA and BIAcore, we were able to triage down to a singlecandidate bo evaluating in-solution behavior, non-specific binding, andbiological activity of the candidates in IgG format without the need tosubclone HC sequences from the original phage vector clones.

Although the foregoing invention has been described in some detail byway of illustration and example for purposes of clarity ofunderstanding, the descriptions and examples should not be construed aslimiting the scope of the invention. The disclosures of all patent andscientific literature cited herein are expressly incorporated in theirentirety by reference.

1-72. (canceled)
 73. An antibody produced using a process comprisingculturing a host cell transformed with a vector comprising a nucleicacid molecule encoding a first polypeptide, a second polypeptide, asignal sequence, and a coat protein or adaptor protein, wherein: (a) thefirst polypeptide comprises a variable light chain (VL) domaincomprising a VL-HVR1, a VL-HVR2, and a VL-HVR3; (b) the secondpolypeptide comprises a variable heavy chain (VH) domain comprising aVH-HVR1, a VH-HVR2, and a VH-VHR3; (c) the signal sequence is functionalin both a prokaryotic cell and an eukaryotic cell and is encoded by anucleic acid sequence that is 5′ to the nucleic acid sequence encodingthe first polypeptide and 5′ to the nucleic acid sequence encoding thesecond polypeptide, wherein the signal sequence is encoded by a nucleicacid sequence selected from the group consisting of SEQ ID NO: 11(consensus mBIP sequence, X ATG AAN TTN ACN GTN GTN GCN GCN GCN CTN CTNCTN CTN GGN GCN GTN CGN GCN, wherein N=A, T, C or G, and wherein X=ATG,X=ATG ACC, or Xis absent), SEQ ID NO: 16 (Opt1, ATG ATG AAA TTT ACC GTTGTT GCT GCT GCT CTG CTA CTT CTT GGA GCG GTC CGC GCA), SEQ ID NO: 17(Opt2, ATG ATG AAA TTT ACT GTT GTT GCG GCT GCT CTT CTC CTT CTT GGA GCGGTC CGC GCA), or SEQ ID NO: 18 (Opt 3, ATG ATG AAA TTT ACT GTT GTC GCTGCT GCT CTT CTA CTT CTT GGA GCG GTC CGC GCA); and (d) the firstpolypeptide and the second polypeptide form a full-length antibody,wherein the first and/or second polypeptide is fused to the coat proteinor the adaptor protein.
 74. The antibody of claim 73, wherein theprocess further comprises recovering the antibody expressed by the hostcell.
 75. The antibody of claim 73, wherein the antibody is recoveredfrom the host cell culture medium.
 76. The antibody of claim 73, whereinthe nucleic acid sequence encoding the signal sequence is operablylinked to the 5′ end of the nucleic acid sequence encoding the firstpolypeptide and the 5′ end of the nucleic acid sequence encoding thesecond polypeptide.
 77. The antibody of claim 73, wherein the VL domainand the VH domain are each linked to a utility peptide.
 78. The antibodyof claim 77, wherein the VH domain is linked to a CH1 domain and the VLdomain is linked to a CL domain.
 79. The antibody of claim 78, whereinthe utility peptide is selected from the group consisting of an Fc, atag, a label, and a control protein.
 80. The antibody of claim 79,wherein the VL domain is linked to a control protein and the VH domainis linked to the Fc.
 81. The antibody of claim 73, wherein the nucleicacid encoding the first polypeptide or the second polypeptide is fusedto a synthetic intron, wherein the synthetic intron comprises a nucleicacid encoding the coat protein or adaptor protein.
 82. The antibody ofclaim 81, wherein the synthetic intron is located between a nucleic acidencoding a VH domain and a nucleic acid encoding an Fc or a hinge. 83.The antibody of claim 82, wherein the synthetic intron further comprisesa nucleic acid encoding a naturally occurring intron of IgG1.
 84. Theantibody of claim 81, wherein the nucleic acid encodes an adaptorprotein, and wherein: (a) the adaptor protein is a leucine zipper; or(b) the adaptor protein comprises the amino acid sequence of SEQ ID NO:8, 9, 12, 13, 14, or
 15. 85. The antibody of claim 81, wherein thenucleic acid encodes a coat protein, and wherein the coat protein isselected from the group consisting of pI, pII, pIII, pIV, pV, pVI, pVII,pVIII, pIX, and pX of bacteriophage M13, f1, or fd.
 86. The antibody ofclaim 85, wherein a first Fab fusion protein is expressed in prokaryoticcells and a second Fab fusion protein is expressed in eukaryotic cells.87. The antibody of claim 86, wherein the first Fab fusion protein is aFab-phage fusion protein.
 88. The antibody of claim 87, wherein theFab-phage fusion protein comprises VH/CH1 fused to the pill.
 89. Theantibody of claim 86, wherein the second fusion is a Fab-Fc or aFab-hinge-Fc fusion protein.
 90. The antibody of claim 89, wherein theFab-Fc or the Fab-hinge-Fc fusion protein comprises VH/CH1 fused to anFc.
 91. The antibody of claim 78, wherein the CH1 domain comprises aportion of a natural splice donor sequence.
 92. The antibody of claim79, wherein the Fc comprises a portion of a natural splice acceptorsequence.